title: CELLDATA RNAstorm FFPE RNA Extraction Method-Rep 8

city: Rochester

first: Jin Sung

last: Jang

address: 200 1st st sw

institute: Mayo Clinic

description:
rh2957_R
CELLDATA RNAstorm FFPE RNA Extraction Kit with protocol modifications on the lysis step(Method BL)-Rep 8

data_processing:
FASTQ files were uploaded into Partek Flow software (Partek Inc., USA) for primary QC. The STAR (2.7.8a) aligner was used to align reads to the Macaca mulatta (Mmul_10) reference genome. The generated BAM files were quantified using Partek E/M algorithm (Xing et al, Nucleic Acids Res. 2006;34(10):3150–60) by Ensembl annotations (Ensembl Transcripts release 110) and then normalized using Median of ratios method (M Love, Genome Biol. 2014 15:550). The BAM files were also used for rRNA quantification, calculated using the percentage of the total mapped reads using Partek E/M algorithm.
Assembly: Mmul_10
Supplementary files format and content: xlsx, raw gene counts

organism: Macaca mulatta

source_name: Cardiac Tissue

extract_protocol:
Qiagen AllPrep DNA/RNA FFPE kit, with protocol modification on the ethanol wash step after deparaffinization(Method QE)
Illumina Stranded Total RNA-seq kit, Ligation
Total RNA-seq

tag: method

value: Cardiac Tissue


title: Qiagen AllPrep DNA/RNA FFPE kit- Rep 8

status: Public on May 23 2024

type: SRA

country: USA

description:
rh2957
Qiagen AllPrep DNA/RNA FFPE kit, with protocol modification on the ethanol wash step after deparaffinization(Method QE)-Rep 8

library_source: transcriptomic

molecule: total RNA

tag: tissue


title: SEnd_seq of total RNA from Mtb cells  upon  rho  knockdown 96 h and 20 min DMSO treatment, replicate 2

city: Newyork

first: Shixin

last: Liu

state: NY

address: 1230 York AV

institute: The Rockefeller University

data_processing:
Basecalls performed using bcl2fastq ver 2.16 for NextSeq paired reads.
Paired-end reads were merged to single end fasta reads by usin FlASh software v1.2.11
Labled transcript 5' end and 3' end were extracted from merged single end reads and processed to paired-end reads again by custom program scripts
Extracted paired-end reads were mapped to Mtb(NC_018143.2 ) by using Bowtie2 v2.5.1, and single end full length sequence was generated by  the paried-end data by custome transcripts and Bowtie2.
rRNA transcripts were removed and TSSs, TTSs and overlap TTSs were extracted from the remaining data.
Assembly: Mycobacterium tuberculosis H37RV, NC_018143.2
Supplementary files format and content: wig files for RNA coverage
Library strategy: SEnd-seq

organism: Mycobacterium tuberculosis

source_name: bacterial cell

growth_protocol: Mycobacterium tuberculosis (Mtb) H37Rv was grown at 37 °C in a minimal medium (Difco Middlebrook 7H9 broth) supplemented with 0.5% (v/v) glycerol, 0.05% (v/v) tyloxapol, 0.2 g L-1 casamino acids, 0.024 g L-1 pantothenic acid and 10% (v/v) OADC (BD). The double auxotrophic Mtb mc2 6206 strain (H37Rv ΔpanCD ΔleuCD)21 was grown in minimal medium with an additional 50 mg L-1 L-leucine (Sigma) and 24 mg mL-1  pantothenic acid (Sigma). 100 ng mL-1 of ATc was added to induce the sgRNA or gene expression if needed.

extract_protocol:
Bacterial cells were quenched by adding 1x vol of GTC buffer (600 g L-1 guanidium thiocyanate, 5 g L-1 N-laurylsarcosine and 7.1 g L-1 sodium citrate and 0.7% (v/v) 2-mercaptoethanol) to the culture medium immediately before the harvest and placed it at room temperature for 15 min. Cell pellets were collected by centrifugation (4,000 g for 10 min at 4 °C), then thoroughly resuspended in 100 μl of TE buffer (10 mM Tris-HCl and 1 mM EDTA, pH8.0). After adding 1 ml of TRIzol Reagent (Invitrogen, 15596) and 300 mg of glass beads (Sigma,  G1145), the cells were immediately lysed by bead beating with the Precellys Evolution homogenizer at the highest speed 10,000 rpm for 4x 45s cycles with interval of 60s at 4°C. Then the RNA was extracted following TRIzol RNA purification protocol.
SEnd-seq strategy was used to prepare the SEnd-seq library

treatment_protocol: The cells were treated with 100 ng/ml ATc, 50 µg/ml rifampicin, 30 µg/ml of linezolid or equal volume of DMSO if needed.

tag: strain

tag: cell type

value: bacterial cell

tag: genotype

value: ATc inducible rho kd

tag: treatment

value: ATc +DMSO

tag: fraction

value: total RNA


title: cHiC of element B deletion in mouse ESC at the Zfp608 locus_R1

city: Montpellier

first: Ivana

last: Jerkovic

state: Occitanie

address: 141 rue de la Cardonille

country: France

institute: IGH, CNRS

library_source: genomic

data_processing:
Hi-C data was processed using the TADbit tool (https://github.com/3DGenomes/tadbit). In brief, raw sequencing reads were mapped independently to the reference genome using Bowtie2 in local alignment mode and non-informative reads were removed using the default options. See adjoning paper for the detailed pipeline.
Assembly: mm10
Supplementary files format and content: Each processed file represent pairwise information of the observed genome contacts. For score files: the data was analyzed with "misha" (https://github.com/tanaylab/misha) database entry and scores were generated using the "shaman" pipeline (https://github.com/tanaylab/shaman). The .mcool files were produced using the cooler package (https://cooler.readthedocs.io/en/latest/index.html).

molecule: genomic DNA

organism: Mus musculus

growth_protocol: ESC were grown in FBS+LIF media with standard conditions. NPCs were differentiated using retinoic acid between days 4 and 8 when the cells were harvested. For detailed protocol see adjoning paper.

extract_protocol:
Cell lysis, digestion, ligation, sonication and biotin labeling was preformed as in in-situ Hi-C protocol from Rao et al 2014. The rest of the protocol was done with SureSelect Agilent capture kit and custom capture library. For detailed protocol see adjoning paper.
Libraries were prepared with the SureSelect Agilent kit. For detailed protocol see adjoning paper.
cHi-C

tag: cell line

value: mESC dB

value: deletion of element B


title: SEnd_seq of total RNA from Mtb cells  upon  rho  knockdown 96 h and 20 min DMSO treatment, replicate 1


title: COLO320, HSR, TPL, input, rep1

city: Stanford

first: Guiping

last: Wang

address: 256 Campus Dr

institute: Stanford University

data_processing:
*library strategy: Kethoxal-assisted single-stranded DNA sequencing (KAS-seq)
The sequence data were mapped to the hg38 assembly of the human genome using Bowtie19,20 with the following settings: -v 2-k 2-m 1--best--strata-X 1000.
Duplicate reads were removed using picard-tools (version 1.99).
MACS221 (v.2.1.1) was used for peak-calling with the following parameters: --broad -g hs --broad-cutoff 0.01 -q 0.01.
macs2 peaks were filtered to within ecDNA intervals.
Assembly: hg38
Supplementary files format and content: Bigwig (.bw) files containing normalized KAS-seq signal to input were generated for visualization.

organism: Homo sapiens

growth_protocol: 4.5 g/L glucose formulated Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% FBS and 1% pen/strep.

extract_protocol:
Genomic DNA was then extracted using the Monarch gDNA Purification Kit (NEB T3010S) following the standard protocol but with elution using 50 µL 25 mM K3BO3 at pH 7.0.
Click reaction was carried out by mixing 87.5 µL purified DNA, 2.5 µL 20 mM DBCO-PEG4-biotin (DMSO solution, Sigma 760749), and 10 µL 10× PBS in a final volume of 100 µL. The reaction was then incubated at 37◦C for 90 minutes. DNA was purified using AMPure XP beads by adding 50 µL beads 100 µL reaction, washing beads on a magnetic stand twice with 80% EtOH, and eluting in 130 µL 25mM K3BO3. Purified DNA was then sheared using a Covaris E220 instrument down to ∼200-400 bp size. Pulldown of biotin-labeled DNA was initiated by separating 10 µL of 10 mg/mL Dynabeads MyOne Streptavidin T1 beads (Life Technologies, 65602) on a magnetic stand, then washing with 180 µL of 1× TWB (Tween Washing Buffer; 5 mM Tris-HCl pH 7.5; 0.5 mM EDTA; 1 M NaCl; 0.05% Tween 20). Beads were then resuspended in 300 µL of 2× Binding Buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA; 2 M NaCl), sonicated DNA was added (diluted to a final volume of 300 µL if necessary), and beads were incubated for ≥15 minutes at room temperature on a rotator. Beads were separated on a magnetic stand and washed with 300 µL of 1× TWB and heated at 55◦C in a Thermomixer with shaking at 1,000 rpm for 2 minutes. The supernatant was removed on a magnetic stand, and the TWB wash and 55◦C incubation were repeated.   Libraries were prepared on beads using the NEBNext Ultra II DNA Library Prep Kit (NEB, #E7645).

treatment_protocol: cell culture media was supplemented with 5 mM N3-kethoxal , and cells were incubated for 10 minutes at 37◦C in a 6-well plate.

value: colorectal carcinoma

value: 1uM triptolide for 3hr


title: SEnd-seq of total RNA without rpoc-his induction, replicate 2

value: Atc inducible rpoC-his

value: MeOH


title: Qiagen AllPrep DNA/RNA FFPE kit- Rep 7

description:
rh2740
Qiagen AllPrep DNA/RNA FFPE kit, with protocol modification on the ethanol wash step after deparaffinization(Method QE)-Rep 7


title: COLO320, DM, TPL, input, rep2


title: cHiC of element A deletion in mouse ESC at the Zfp608 locus_R2

value: mESC dA

value: deletion of element A


title: COLO320, DM, TPL, input, rep1


title: SEnd_seq of total RNA from Mtb cells  without  rho  knockdown 96 h and 20 min linezolid treatment, replicate 2

value: MeOH +Linezolid


title: SEnd_seq of total RNA from Mtb cells  without  rho  knockdown 96 h and 20 min linezolid treatment, replicate 1


title: Bladder tissue biopsy from IC/BPS patient 3

city: Shanghai

first: Fei

last: Su

state: Shanghai

address: 800 Dongchuan Road

department: School of Life Science and Biotechnology

country: China

institute: Shanghai Jiao Tong University

data_processing:
Basecalls performed using CASAVA
Data analysis was performed with CellRanger 3.0
Genome_build: Hg38
Supplementary_files_format_and_content: mtx files were generated from CellRanger
Supplementary_files_format_and_content: tsv files were generated from CellRanger

source_name: Bladder tissue

extract_protocol: Single-cell suspensions were converted to barcoded scRNA-seq libraries by using the Chromium Single Cell 3’ Library, Gel Bead & Multiplex Kit, and Chip Kit (10X Genomics), aiming for an estimated 10,000 cells per library. Samples were processed using kits pertaining to V3 barcoding chemistry of 10X Genomics.

treatment_protocol: No treatment was performed

value: Bladder

tag: disease state

value: Interstitial cystitis/bladder pain syndrome with Hunner lesions

tag: group

value: HIC


title: SEnd_seq of total RNA from Mtb cells  upon  rho  knockdown 96 h and 20 min Rifampicin treatment, replicate 2

value: ATc +Rifampicin


title: COLO320, HSR, DMSO, input, rep2

value: DMSO vehicle for 3hr


title: cHiC of polyA insertion at Zfp608 in mouse ESC at the Zfp608 locus_R2

value: mESC polyA

value: polyA insertion at Zfp608 TSS


title: COLO320, HSR, DMSO, input, rep1


title: cHiC of polyA insertion at Zfp608 in mouse ESC at the Zfp608 locus_R1


title: SEnd_seq of total RNA from Mtb cells  without  rho  knockdown 96 h and 20 min Rifampicin treatment, replicate 2

value: bacterial cell

value: ATc inducible rho kd

value: MeOH +Rifampicin

value: total RNA


title: cHiC of Zfp608 promoter deletion in mouse ESC at the Zfp608 locus_R2

value: mESC dprom

value: deletion Zfp608 promoter


title: COLO320, DM, DMSO, input, rep2

value: colorectal carcinoma


title: Qiagen AllPrep DNA/RNA FFPE kit- Rep 4

description:
r15089
Qiagen AllPrep DNA/RNA FFPE kit, with protocol modification on the ethanol wash step after deparaffinization(Method QE)-Rep 4

value: Cardiac Tissue


title: Qiagen AllPrep DNA/RNA FFPE kit- Rep 5

description:
r16010
Qiagen AllPrep DNA/RNA FFPE kit, with protocol modification on the ethanol wash step after deparaffinization(Method QE)-Rep 5


title: CELLDATA RNAstorm FFPE RNA Extraction Method-Rep 7

description:
r15089_R
CELLDATA RNAstorm FFPE RNA Extraction Kit with protocol modifications on the lysis step(Method BL)-Rep 7


title: SEnd_seq of total RNA from Mtb cells  without  rho  knockdown 96 h and 20 min DMSO treatment, replicate 2

value: MeOH +DMSO


title: COLO320, HSR, TPL, KAS, rep2

value: 1uM triptolide for 3hr


title: COLO320, DM, DMSO, input, rep1


title: CELLDATA RNAstorm FFPE RNA Extraction Method-Rep 6

description:
r15045_R
CELLDATA RNAstorm FFPE RNA Extraction Kit with protocol modifications on the lysis step(Method BL)-Rep 6


title: Qiagen AllPrep DNA/RNA FFPE kit- Rep 3

description:
r15045
Qiagen AllPrep DNA/RNA FFPE kit, with protocol modification on the ethanol wash step after deparaffinization(Method QE)-Rep 3


title: cHiC of wt mouse ESC at the Zfp608 locus_R2

value: mESC wt

value: Wild type


title: cHiC of Zfp608 promoter deletion in mouse ESC at the Zfp608 locus_R1


title: COLO320, HSR, TPL, KAS, rep1


title: SEnd-seq of Nascent RNA after rpoc-his induction, replicate 4

data_processing:
Basecalls performed using bcl2fastq ver 2.16 for NextSeq paired reads.
Paired-end reads were merged to single end fasta reads by usin FlASh software v1.2.11
Labled transcript 5' end and 3' end were extracted from merged single end reads and processed to paired-end reads again by custom program scripts
Extracted paired-end reads were mapped to Mtb(NC_018143.2 ) by using Bowtie2 v2.5.1, and single end full length sequence was generated by  the paried-end data by custome transcripts and Bowtie2.
Data analysis with custom scripts.
Assembly: Mycobacterium tuberculosis H37RV, NC_018143.2
Supplementary files format and content: wig files for RNA coverage
Library strategy: SEnd-seq

extract_protocol:
The cell culture was mixed with an equal volume of frozen 2× crush buffer (20 mM Tris-HCl pH 7.8, 10 mM EDTA, 100 mM NaCl, 1 M Urea, 25 mM NaN3, 2 mM β-mercaptoethanol, 10% ethanol, 0.4% NP40, and 1 mM PMSF) to stabalize RNAP complex. After immobilization with Ni-NTA agarose and thorough washing, the RNA was extracted through elution with 300 mM of imidazole. The RNA was further treated with DNase and cleaned with phenol-chloroform before library preparation.
SEnd-seq strategy was used to prepare the sequencing libraries.

treatment_protocol: RNA  samples were collected when Mtb cells treated with control MeOH or ATc respectively.

value: Atc inducible rpoC-his

value: Atc

value: Nascent RNA


title: SEnd_seq of total RNA from Mtb cells  without  rho  knockdown 96 h and 20 min DMSO treatment, replicate 1


title: cHiC of wt mouse ESC at the Zfp608 locus_R1


title: CELLDATA RNAstorm FFPE RNA Extraction Method-Rep 5

description:
I30_B
CELLDATA RNAstorm FFPE RNA Extraction Kit with protocol modifications on the lysis step(Method BL)-Rep 5


title: cHiC of element A deletion in mouse ESC at the Zfp608 locus_R1

value: mESC dA

value: deletion of element A


title: SEnd-seq of Nascent RNA after rpoc-his induction, replicate 3

value: bacterial cell


title: Qiagen AllPrep DNA/RNA FFPE kit- Rep 6

description:
r16116
Qiagen AllPrep DNA/RNA FFPE kit, with protocol modification on the ethanol wash step after deparaffinization(Method QE)-Rep 6


title: CELLDATA RNAstorm FFPE RNA Extraction Method-Rep 4

description:
16116_B
CELLDATA RNAstorm FFPE RNA Extraction Kit with protocol modifications on the lysis step(Method BL)-Rep 4


title: SEnd-seq of Nascent RNA after rpoc-his induction, replicate 2


title: Lactuca sativa, stem, s2, NGS, RNAseq

city: Guangzhou

first: Zhuoxing

last: Shi

state: GD

address: #7 Jinsui Road, Tianhe District

department: State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center

institute: Sun Yat-sen University

description: NGS

data_processing:
HIT-ISOseq analysis software kit (https://github.com/shizhuoxing/Lettuce_HIT-ISOseq_Paper) for Full-Length Non-Concatemer (FLNC) reads identification, UMI extraction and correction.
Assembly: Lsat_Salinas_v7
Supplementary files format and content: Tab-separated values files and fasta files

molecule: polyA RNA

organism: Lactuca sativa

source_name: stem

extract_protocol:
The  amplification procedure refer to HIT-ISOseq.
The  library construction procedures refer to HIT-ISOseq.

value: stem

value: garden lettuce

value: bulk


title: COLO320, DM, TPL, KAS, rep2


title: CELLDATA RNAstorm FFPE RNA Extraction Method-Rep 3

description:
16010_B
CELLDATA RNAstorm FFPE RNA Extraction Kit with protocol modifications on the lysis step(Method BL)-Rep 3


title: COLO320, DM, TPL, KAS, rep1


title: SEnd_seq of total RNA from Mtb cells  without  rho  knockdown 96 h and 20 min Rifampicin treatment, replicate 1

value: ATc inducible rho kd

value: MeOH +Rifampicin

value: total RNA


title: Lactuca sativa, stem, s1, NGS, RNAseq

description: NGS


title: COLO320, HSR, DMSO, KAS, rep2

value: colorectal carcinoma

value: DMSO vehicle for 3hr


title: CELLDATA RNAstorm FFPE RNA Extraction Method-Rep 2

description:
12075_B
CELLDATA RNAstorm FFPE RNA Extraction Kit with protocol modifications on the lysis step(Method BL)-Rep 2

value: Cardiac Tissue


title: Lactuca sativa, leaf, s2, NGS, RNAseq

description: NGS

source_name: leaf

value: leaf


title: CELLDATA RNAstorm FFPE RNA Extraction Method-Rep 1

description:
2740_B
CELLDATA RNAstorm FFPE RNA Extraction Kit with protocol modifications on the lysis step(Method BL)-Rep 1


title: COLO320, HSR, DMSO, KAS, rep1


title: SEnd-seq of Nascent RNA after rpoc-his induction, replicate 1


title: Lactuca sativa, leaf, s1, NGS, RNAseq

description: NGS


title: COLO320, DM, DMSO, KAS, rep2


title: Lactuca sativa, root, s2, NGS, RNAseq

description: NGS

source_name: root

value: root


title: Qiagen AllPrep DNA/RNA FFPE kit- Rep 2

description:
2-rhbi30
Qiagen AllPrep DNA/RNA FFPE kit, with protocol modification on the ethanol wash step after deparaffinization(Method QE)-Rep 2


title: COLO320, DM, DMSO, KAS, rep1


title: Qiagen AllPrep DNA/RNA FFPE kit- Rep 1

description:
2-r12075
Qiagen AllPrep DNA/RNA FFPE kit, with protocol modification on the ethanol wash step after deparaffinization(Method QE)-Rep 1


title: Lactuca sativa, root, s1, NGS, RNAseq

description: NGS


title: HYDROX-cultured human liver organoids-1

status: Public on May 22 2024

city: Suita

first: Yanran

last: Tong

state: Osaka

address: 1-6, Yamadaoka

department: Graduate School of Pharmaceutical Sciences

country: Japan

institute: Osaka University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic.
Trimmed sequence reads were mapped to GRCh38 using HISAT2.
Read count extraction and nomalization were performed using samtools and featureCounts.
Supplementary files format and content: tab-delimited text file includes raw conuts for each Sample.

source_name: human liver organoids

growth_protocol: Human liver organoids culture medium was prepared according to the previous report [Huch et al., Cell, 2015]. Briefly, Advanced DMEM/F12 was supplemented with 1% Antibiotic Antimycotic Solution and 1% GlutaMAX (GIBCO), 10 mM HEPES (Nacalai Tesque), 2% B27 supplement (GIBCO), 1.25 mM N-Acetylcysteine (Sigma), 10 mM Nicotinamide (Sigma), 10 nM recombinant gastrin (Merk), 50 ng/ml EGF (R&D), 10% R-Spondin1 conditioned medium (homemade), 100 ng/ml recombinant human FGF10 (PeproTech), 25 ng/ml recombinant human HGF (R&D), 5 uM A83-01 (Wako), and 10 uM Forskolin (Wako). During cultivation, medium was refreshed every three days. For the establishment of human liver organoids, the medium was supplemented with 25 ng/ml recombinant Noggin (R&D), 7.5 ng/mL recombinant Wnt3a (R&D) and 10 uM Y27632 (Wako) for the first 3-4 days. Passage was performed in a 1:3 split ratio once every 10–14 days. Organoids passaged 5–10 times were used in all experiments

extract_protocol:
RNA was extracted using RNeasy Mini Kit.
According to the manufacturer's instructions, library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA). Libraries were converted to libraries for DNBSEQ using MGIEasy Universal Library Conversion Kit (App-A).

treatment_protocol: PSar-PLLA polymer was synthesized as described previously [Matsui et al., Mater. Today Commun., 2017], with 109 sarcosine units and 33 lactic acid units per molecule.  Dried gels were prepared with a modified protocol as described previously [Enomoto et al., ACS Appl. Bio Mater., 2021]. Briefly, PSar-PLLA polymers was dissolved in 1 mL of 95% ethanol (Fujifilm Wako Pure Chemicals,) and then heated using a block incubator at 70°C for 5 min. Next, polymer solution was poured in a 48-well culture plate (Corning). Dried gels were obtained by drying at room temperature overnight to remove ethanol solvents. These coated plates were stored at room temperature before use. Human liver organoids were collected and incubated in TrypLE select at 37°C for 7–10 min to dissolve the Matrigel. After incubation, the cells were pipetted up and down to dissociate organoids. Then human liver organoids were seeded and cultured for 7 days on a 10 mg/mL dried gel coated 48-well plate in the human liver organoids culture media described above.

value: human liver organoids

value: cultured cell

value: HYDROX-culture


title: HYDROX-cultured human liver organoids-2


title: SEnd-seq of Nascent RNA without rpoc-his induction, replicate 1

value: Atc inducible rpoC-his

value: MeOH

value: Nascent RNA


title: Matrigel-cultured human liver organoids-3


title: SEnd-seq of Nascent RNA without rpoc-his induction, replicate 2

value: bacterial cell


title: Matrigel-cultured human liver organoids-1


title: Matrigel-cultured human liver organoids-2


title: SKNMC_FTP_1

type: genomic

city: Heidelberg

first: Thomas

middle: Georg Philipp

last: Grunewald

address: Im Neuenheimer Feld 280

department: Division of Translational Pediatric Sarcoma Research

country: Germany

institute: German Cancer Research Center (DKFZ)

hyb_protocol: DNA was bisulfite converted, amplified, fragmented, and hybridised to Illumina Infinium MethylationEPIC BeadChip arrays following manufacturer's protocol

scan_protocol: Illumina protocol

data_processing:
The initial pre-processing of the raw methylation was performed in R version 3.3.1. Raw signal intensities were obtained from IDAT-files using the minfi Bioconductor package version 1.21.4 in R version 3.3.1. Each sample was individually normalized by performing a background correction (shifting of the 5% percentile of negative control probe intensities to 0) and a dye-bias correction (scaling the mean of normalization control probe intensities to 10,000) for both color channels. The methylated and unmethylated signals were corrected individually. Subsequently, beta values were calculated from the retransformed intensities using an offset of 100 (as recommended by Illumina). Out of 865,859 probes on the EPIC array, 105,454 probes were masked according to Zhou et al. as well as 16,944 probes on the X and Y chromosomes. In total, 743,461 probes were kept for downstream analysis. The beta values were transformed to M-values with the logit2 function of the minfi package version 1.42.0, R version 4.2.0.
processed data file contains: Average Beta

label: cy3 and cy5

source_name: genomic DNA from SKNMC_FTP_1

label_protocol: cy3, cy5

growth_protocol: All cell lines were cultured at 37 °C, 5% CO2 in RPMI 1640 (Biochrom, Germany) supplemented with 10% fetal bovine serum (Sigma-Aldrich, Germany) and 1% penicillin-streptomycin (Merck, Germany).

extract_protocol: When flasks reached approximately 70% confluency, samples were lysed, and total DNA was extracted with the NucleoSpin Tissue kit (Macherey Nagel) following the manufacturer’s protocol.

treatment_protocol: Not applicable.

value: SKNMC


title: MCF7_FTP

source_name: genomic DNA from HELA_2018_3

value: HELA


title: SKNMC_FTP

source_name: genomic DNA from SKNMC_FTP


title: HeLa_InaO

source_name: genomic DNA from HELA_2018_4


title: HeLa_FTP

source_name: genomic DNA from HELA_2018_2


title: HeLa_AJ

source_name: genomic DNA from HELA_2018_5


title: MHH-ES1_MTP_1

source_name: genomic DNA from MHH-ES1_MTP_1


title: MHH-ES1_MTP

source_name: genomic DNA from MHH-ES1_MTP


title: SKNMC_ITP_1

source_name: genomic DNA from SKNMC_ITP_1


title: SKNMC_ITP

source_name: genomic DNA from SKNMC_ITP


title: SEnd-seq of Nascent RNA without rpoc-his induction, replicate 3


title: MCF7_2011_1

source_name: genomic DNA from MCF7_2011_1


title: MHH-ES1_FTP_1

source_name: genomic DNA from MHH-ES1_FTP_1


title: MCF7_2011

source_name: genomic DNA from MCF7_2011


title: HYDROX-cultured human liver organoids-3


title: MHH-ES1_FTP

source_name: genomic DNA from MHH-ES1_FTP


title: MHH-ES1_ITP_1

source_name: genomic DNA from MHH-ES1_ITP_1


title: SKES_MTP

source_name: genomic DNA from SKES_MTP

value: SKES


title: SKES_MTP_1

source_name: genomic DNA from SKES_MTP_1


title: SKES_ITP

source_name: genomic DNA from SKES_ITP


title: MCF7_2004_1

source_name: genomic DNA from MCF7_2004_1


title: TC71_MTP_1

source_name: genomic DNA from TC71_MTP_1


title: SKES_FTP

source_name: genomic DNA from SKES_FTP


title: TC71_MTP

source_name: genomic DNA from TC71_MTP


title: MCF7_2004

source_name: genomic DNA from MCF7_2004


title: SKES_ITP_1

source_name: genomic DNA from SKES_ITP_1


title: MHH-ES1_ITP

source_name: genomic DNA from MHH-ES1_ITP


title: HELA_0_MTP_1

source_name: genomic DNA from HELA_0_FTP_1


title: SKES_FTP_1

source_name: genomic DNA from SKES_FTP_1


title: A673_MTP

source_name: genomic DNA from A673_MTP


title: A673_MTP_1

source_name: genomic DNA from A673_MTP_1


title: TC71_FTP

source_name: genomic DNA from TC71_FTP


title: HELA_0_MTP

source_name: genomic DNA from HELA_0_FTP


title: TC71_FTP_1

source_name: genomic DNA from TC71_FTP_1


title: A673_FTP_1

source_name: genomic DNA from A673_FTP_1


title: A673_ITP_1

source_name: genomic DNA from A673_ITP_1


title: A673_ITP

source_name: genomic DNA from A673_ITP


title: MCF7_0_MTP_1

source_name: genomic DNA from MCF7_0_FTP_1


title: HELA_0_ITP

source_name: genomic DNA from HELA_0_ITP


title: HELA_0_ITP_1

source_name: genomic DNA from HELA_0_ITP_1


title: TC71_ITP

source_name: genomic DNA from TC71_ITP


title: MCF7_0_ITP_1

source_name: genomic DNA from MCF7_0_ITP_1


title: A673 KS_ITP

source_name: genomic DNA from A673 KS_ITP


title: MCF7_0_MTP

source_name: genomic DNA from MCF7_0_FTP


title: TC71_ITP_1

source_name: genomic DNA from TC71_ITP_1


title: A673 KS_ITP_1

source_name: genomic DNA from A673 KS_ITP_1


title: A673 TG_ITP_1

source_name: genomic DNA from A673 TG_ITP_1


title: A673 HK_ITP_1

source_name: genomic DNA from A673 HK_ITP_1


title: MCF7_0_ITP

source_name: genomic DNA from MCF7_0_ITP


title: A673 HK_ITP

source_name: genomic DNA from A673 HK_ITP


title: A673 TG_ITP

source_name: genomic DNA from A673 TG_ITP


title: A673 UTA_ITP_1

source_name: genomic DNA from A673 UTA_ITP_1


title: A673/SHEF_ITP

source_name: genomic DNA from A673/SHEF_ITP


title: A673_FTP

source_name: genomic DNA from A673_FTP


title: A673 UTA_ITP

source_name: genomic DNA from A673 UTA_ITP


title: SKNMC_MTP

source_name: genomic DNA from SKNMC_MTP


title: A673/SHCTRL_ITP_1

source_name: genomic DNA from A673/SHCTRL_ITP_1


title: A673/SHCTRL_ITP

source_name: genomic DNA from A673/SHCTRL_ITP


title: A673 DS_ITP

source_name: genomic DNA from A673 DS_ITP


title: A673 DS_ITP_1

source_name: genomic DNA from A673 DS_ITP_1


title: A673/SHEF_ITP_1

source_name: genomic DNA from A673/SHEF_ITP_1


title: A673 EDA_ITP_1

source_name: genomic DNA from A673 EDA_ITP_1


title: A673 EDA_ITP

source_name: genomic DNA from A673 EDA_ITP


title: SKNMC_MTP_1

source_name: genomic DNA from SKNMC_MTP_1


title: genomic DNA from FFPE material of EPN patient biopsie 1

city: Hamburg

first: Julia

middle: Elisabeth

last: Neumann

address: Martinistrasse 52

department: ZMNH

institute: University Hospital Hamburg Eppendorf

description: SAMPLE 1

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation850K/EPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Raw idats files were processed further in Rstudio (version 4.3.1) using minfi package

label: Cy5 and Cy3

source_name: FFPE material of EPN patient biopsie 1

label_protocol: Standard Illumina Protocol

extract_protocol: 100 - 250 ng DNAgenomic DNA was extracted and purified using Illumina FFPE Restore Kit

tag: gender

value: Female

value: novel subtype of spinal ependymoma


title: genomic DNA from FFPE material of EPN patient biopsie 4

description: SAMPLE 4

source_name: FFPE material of EPN patient biopsie 4


title: bulkATACseq_CD34+_CTRL_03h_rep3

city: Paris

first: Laëtitia

last: RACINE

address: 27 rue de Chaligny

institute: EPHE

description: bulk ATAC seq - Fast ATAC protocol

data_processing:
Cleaning and alignment of data using : trimmomatic (v0.32), bowtie2 (v2.4.1), samtools (v1.4), macs2 (v2.1.1), picard (v1.138) and bedtools (v.2.29.2)
Snakemake (v7.25.0) workflow to handle bam files : merge biological donors (samtools merge v1.11), index the files, quality control checking and count reads.
A downsampling step with samtools view function was performed as regard to the smallest number of reads detected in the cohort (80 000 000 reads)
A new peak calling was conducted on downsampled .bam files using the macs2 callpeak tool (v2.2.7.1) with the following parameters: <-f BAMPE -g hs -B –broad –broad-cutoff 0.1>.
R (v4.2.1) & Rsubread (v2.4.0) & GenomicRanges (v1.42.0) & DEseq2 (v1.38.3) & ggplot2 (v3.4.2)
Only peaks with 10 or more reads were kept for further analysis.
Assembly: hg19
Supplementary files format and content: xxx_threshold_10_ann.gr.rds files are genomic ranges object for R scripts. Biological replicates for the same condition and time point were merged and filter on the minimal number of reads per peak was applied.

source_name: Umbilical cord blood

growth_protocol: CD34+ cells were purified from human healthy cord blood with a two-step immunomagnetic beads protocol and were then frozen in a cryopreservation medium. After thawing, CD34+ cells were cultured in a 96-well plate in a humidified 5% CO2 incubator at 37°C. Cells were grown in prestimulation medium made of X-Vivo (Lonza) supplemented with penicillin/streptomycin (respectively 100U/mL and 100µg/mL - Gibco, Thermo Scientific), 50 ng/ml h-FLT3, 25 ng/ml h-SCF, 25 ng/ml h-TPO, 10 ng/ml h-IL3 (Miltenyi) final concentration.

extract_protocol:
Living cells were isolated before transposition by FACS using 7-AAD labeling. Around 5000 cells for each sample were used.
Library was prepared following the Fast ATAC-seq protocol, controled with Bioanalyzer and sequenced with NextSeq or MiSeq system.

treatment_protocol: Cells were stimulated with cytokines after thawing and were grown in the same medium with or without metabolic inhibitor (2-DG, DON or AOA) until lysis was performed. Cells were collected and lysed after 03h, 12h or 24h of cytokine stimulation.

value: Umbilical cord blood

value: Healthy

value: CD34+ cells

value: Untreated


title: bulkATACseq_CD34+_Xvivo_00h_rep3

description: bulk ATAC seq - Fast ATAC protocol

value: Untreated & no cytokins


title: genomic DNA from FFPE material of EPN patient biopsie 3

description: SAMPLE 3

source_name: FFPE material of EPN patient biopsie 3


title: rrp4/urt1/heso1_rep3

city: København N

first: Peter

last: Brodersen

address: Ole Maaløes Vej 5

country: Denmark

institute: University of Copenhagen

description: sRNAseq libraries

data_processing:
The adaptor sequence, AGATCGGAAGAG CACACGTCTGAACTCCAGTCAC, was trimmed from raw reads with cutadapt v.2.4
Reads were mapped with STAR 2.6.0a to TAIR10 with the following parameters: outFilterMultimapNmax 20, alignIntronMax 1, outFilterMismatchNmax 1, outFilterMismatchNoverL max 0, outFilterScoreMinOverLread 0, outFilterMatchN minOverLread 0, outFilterMatchNmin 15, alignSJDBover hangMin 100. No rRNA or tRNA reads were removed prior to mapping.
Mapped reads were quanti!ed with featureCounts from subread-1.6.3 with an Araport11 transcriptome reference !le custom modi!ed to also include intergenic regions.
The package DESeq2 was used for the differential expression analysis. Normalized reads were estimated for size factors and a generalized linear model was used. The DESeq2 results were extracted with manual contrasting of mutant versus WT. A gene was considered to have differentially expressed small RNA levels compared to WT if the Padj < 0.05 as assessed by Wald’s tests.
Assembly: TAIR10 genome was indexed with Arabidopsis_thaliana.TAIR10.49.gff3
Supplementary files format and content: the xlsx file contains the following columns (gene, baseMean, log2FoldChange, pvalue, padj, locus_type, genotype)

organism: Arabidopsis thaliana

source_name: inflorescences

growth_protocol: All seeds were sterilized and germinated on plates containing 1x Murashige & Skoog medium (#M0222.0050, Saveen og Werner ApS, Denmark), supplemented with 1% (w/v) sucrose and 0.8% (w/v) agar. Seedlings were transferred to soil (Plugg/Såjord [seedcompost]; SW Horto, Bramming, Denmark) 10 days after germination (DAG). After transfer to soil, plants were grown in a Percival growth chamber for an additional 4 weeks under the following conditions: 16 h light (Master TL-D 36W/840 and 18W/840 bulbs (Philips); 130 mmol m−2 s−1, 21°C, 60% relative humidity)/ 8 h darkness (16°C, 60% relative humidity).

extract_protocol:
Inflorescences and rosettes for northern blots, western blots and sequencing libraries were collected and snap-frozen in liquid nitrogen. Total RNA from inflorescences was extracted with TRI Reagent (#T9424, Sigma-Aldrich Denmark A/S) according to the manufacturer’s instructions. The RNA was dissolved in nuclease-free water.
1 μg of total inflorescence RNA was used as input in each library. Libraries were generated using the NEBNext Multiplex Small RNA Library Prep Set (#E7300S, New England Biolabs) according to the manufacturer’s instructions. The indexed cDNA libraries were size selected on a 6% polyacrylamide gel as described in the NEBNext protocol. All size-selected libraries were analyzed using an Agilent Bioanalyzer, quantified with Qubit measurements (#Q32854, Invitrogen) and single-end sequenced on an Illumina Nextseq 500 with SE75_HI chemistry (#FC-404-2005, Illumina). 1% of spike-in PhiX Control v3 (#15017666, Illumina) was also loaded.

value: inflorescences


title: rrp4/urt1/heso1_rep2

description: sRNAseq libraries


title: rrp4/urt1/dcl2_rep3

description: sRNAseq libraries


title: genomic DNA from FFPE material of EPN patient biopsie 2

description: SAMPLE 2

source_name: FFPE material of EPN patient biopsie 2


title: rrp4/urt1/dcl2_rep2

description: sRNAseq libraries


title: rrp4/urt1/heso1_rep1

description: sRNAseq libraries


title: heso1/urt1_rep1

description: sRNAseq libraries


title: heso1/urt1_rep2

description: sRNAseq libraries


title: AEM087DX

city: New Orleans

first: Jovanny

last: Zabaleta

state: LA

address: 1700 Tulane Ave

department: Interdisciplinary Oncology

institute: LSUHSC

hyb_protocol: Bisulfite-converted DNA was amplified and hybridized to the Infinium Methylation EPIC Kit chips

scan_protocol: Illumina’s iScan

data_processing: Low-confidence probes (p-value >0.05) and probes mapped to X and Y chromosomes were excluded from the analysis. Normalization was done using NOOB (background correction method with dye-bias normalization for Illumina Infinium methylation arrays).

label: Cy5, Cy3

source_name: Diagnostic Fresh Bone Marrow_MRDposDay15_MRDposEndInduc

extract_protocol: DNA from MACS-sorted blasts were extracted using the Allprep mini kit and the robotic workstation QIAcube (Qiagen, Hilden, Germany) following the manufacturer's protocol

value: Diagnostic Fresh Bone Marrow


title: CMD090

source_name: Diagnostic Fresh Bone Marrow_MRDposDay15_MRDnegEndInduc


title: rrp4/urt1/dcl2_rep1

description: sRNAseq libraries


title: heso1-4_rep1

description: sRNAseq libraries


title: NAC081DX


title: NSH064


title: DFP084MX1


title: ESR082

source_name: Diagnostic Fresh Bone Marrow_MRDnegDay15_MRDnegEndInduc


title: heso1/urt1_rep3

description: sRNAseq libraries


title: KJM086


title: urt1-1_rep2

description: sRNAseq libraries


title: urt1-1_rep1

description: sRNAseq libraries


title: rrp4-2_rep3

description: sRNAseq libraries


title: JMC053


title: DIF054


title: LVC063


title: rrp4-2_rep1

description: sRNAseq libraries


title: LSA023


title: urt1-1_rep3

description: sRNAseq libraries


title: LLC022


title: AFC050DXMX2


title: JLG033


title: JEE037


title: JSR021


title: ski2-5_rep3

description: sRNAseq libraries


title: ski2-5_rep1

description: sRNAseq libraries


title: DSR017


title: MGG080


title: NB075


title: KDA013


title: AFV057MX1


title: JM040


title: CZA072MX1


title: rrp4-2_rep2

description: sRNAseq libraries


title: HCMMX1


title: ski2-5_rep2

description: sRNAseq libraries


title: heso1-4_rep3

description: sRNAseq libraries


title: Col-0_rep1

description: sRNAseq libraries

value: Col-0 WT


title: Col-0_rep3

description: sRNAseq libraries


title: Col-0_rep2

description: sRNAseq libraries


title: JSM026


title: Brain_20Gy_ 5 days_2

type: RNA

city: St Paul

first: Davis

last: Seelig

state: MN

address: 1352 Boyd Ave.

department: Department of Veterinary Clinical Sciences

institute: University of Minnesota

description: 50ng of RNA was used for NanoString nCounter Neuroinflammation Panel

hyb_protocol: A total of 50 nanograms of RNA from each sample was used to evaluate gene expression by the nCounter® Neuroinflammation Panel from NanoString (NanoString Technologies, Seattle, WA, USA) following manufactures protocol (MAN-10023-11 nCounter XT Assay User Manual).

scan_protocol: A total of 50 nanograms of RNA from each sample was used to evaluate gene expression by the nCounter® Neuroinflammation Panel from NanoString (NanoString Technologies, Seattle, WA, USA) following manufactures protocol (MAN-C0035-07, nCounter Analysis System Manual).

data_processing: The nSolver™ Analysis Software version 4.0 (NanoString Technologies, Seattle, WA, USA) quality control parameters were used to assess quality of imaging, binding density, positive control linearity and positive control limit of detection. The nSolver™ Analysis Software Advanced Analysis Module (version 2.0.134) was used to analyze gene expression data, including gene normalization, and differential expression volcano plots with p-values from linear regression. The Advanced Analysis Module was used to normalize raw gene data for each sample to the geometric mean of the endogenous housekeeping genes using the geNorm algorithm. The normalized gene expression data was analyzed using 10.1.2 (GraphPad Software, San Diego, CA,USA). One-way analysis of variance (ANOVA) with the Dunnett  post-hoc test was used to evaluate differences between treatment groups and control mice.

source_name: Brain

extract_protocol: RNA was extracted using the RNeasy Plus Universal Mini kit (Qiagen, Germantown, MD, Cat# 73404) according to manufactures instructions.

treatment_protocol: SKH1 mice were treated with 20Gy or 30Gy hindlimb radation (RT).  Brains were collected and frozen from 3 mice per group including control group (no treatment). RNA was extracted from the frozen brain tissue.

value: Brain

tag: agent

tag: time point

value: 5 days


title: Brain_20Gy_ 24 hours_3

value: 24 hours


title: Brain_30Gy_ 24 hours_1


title: Brain_20Gy_ 24 hours_2


title: Brain_Control_ 24 hours_1

value: Control


title: Brain_Control_ 24 hours_3


title: Brain_20Gy_12 days_3

value: 12 days


title: Brain_20Gy_ 5 days_1


title: Brain_20Gy_ 5 days_3


title: Brain_Control_ 24 hours_2


title: Brain_20Gy_12 days_2


title: Brain_30Gy_ 24 hours_2


title: Brain_20Gy_12 days_1


title: Brain_30Gy_12 days_2


title: Brain_30Gy_12 days_1


title: Brain_Control_12 days_3


title: Brain_30Gy_ 24 hours_3


title: Brain_Control_12 days_1


title: Brain_30Gy_ 5 days_3


title: Honey possum (Sample1785)

city: Houston

first: Olga

last: Dudchenko

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

description: RagTag

data_processing:
Short-read assembly using w2rap (Clavijo, 2017); Hi-C-guided genome assembly (Juicer, 3D-DNA, JBAT); RagTag assembler (Alonge et al., 2022) for Dactylopsila trivirgata and Distoechurus pennatus
Assembly: Generated as part of the study
Supplementary files format and content: fasta.gz: chromosome-length nucleotide sequences generated usign Hi-C-guided genome assembly; RagTag assisted assemblies for Dactylopsila trivirgata and Distoechurus pennatus
Library strategy: In situ Hi-C; ClaSeek PCR-free DNA-Seq.

organism: Tarsipes rostratus

source_name: kidney

extract_protocol:
Extractions for WGS libraries were done using DNeasy blood & tissue kit
The Hi-C libraries were prepared following the in situ Hi-C strategy (Rao, Huntley et al., 2014). Briefly, cells or tissue were crosslinked and then lysed with nuclei permeabilized but still intact. DNA was then restricted and the overhangs filled in incorporating a biotinylated base. Free ends were then ligated together in situ. Crosslinks were reversed, the DNA was sheared to 300-500bp and then biotinylated ligation junctions were recovered with streptavidin beads. Afterward DNA was handled according to standard Illumina library construction protocol. DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo-) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3 end. After adapter ligation DNA was PCR amplified with Illumina primers and library fragments of 400-600 bp (insert plus adaptor and PCR primer sequences) were purified using SPRI beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on various Illumina instruments following the manufacturer's protocols. Fpr the tammar wallaby, a short insert-size PCR-free DNA-Seq library was prepared following the ClaSeek protocol.

value: kidney


title: Greater glider (Sample1768)

organism: Petauroides volans


title: Brain_30Gy_12 days_3


title: Brain_30Gy_ 5 days_2


title: Brain_30Gy_ 5 days_1


title: Eastern grey kangaroo (Sample1143)

organism: Macropus giganteus

source_name: blood

value: blood


title: Hi-C of Elephas maximus DNA Zoo Sample0030, part2

description:
HIC1381_ASM1433276v1_HiC.hic
HIC1381_ASM1433276v1_HiC_30.hic

data_processing:
Hi-C-guided genome assembly (3D-DNA, JBAT)
Reference-guided 3D genome assembly (Anonamos, 3D-DNA, JBAT)
Construction of the chromosome-length Hi-C contact map (BWA, Juicer, 3D-DNA)
liftover (KentUtils, 3D-DNA)
Gene annotation (TOGA)
Compartment annotation (CRUSH)
Loop calling and aggregate analysis (HiCCUPS, Juicer Tools, SIP, SIP META)
Aggregate chromosome analysis (3D-DNA)
Modeling of 3D structures of woolly mammoth chromosomes (OpenMiChroM)
DNA degradation simulations (NuChroM, custom script)
Assembly: The following existing genome builds were used in parts of the study: Loxafr3.0 (GCA_000001905.1), ASM1433276v1 (GCA_014332765.1), EquCab2.0 (GCF_000002305.2), ASM303372v1 (GCA_003033725.1), bosTau9 (GCF_002263795.3), ASM651725v1 (GCF_006517255.1), ASM3043605v1 (GCF_030436055.1), ASM331443v2 (GCF_003314435.2), hg38, hg19.
Supplementary files format and content: fasta.gz: chromosome-length nucleotide sequences generated usign Hi-C-guided genome assembly
Supplementary files format and content: hic: contact maps generated by aligning Hi-C data to reference sequences. In addition to "standard" hic maps build against chromosome-length references included are "assembly" maps generated by 3D-DNA for before and after genome assembly and an aggregate chromosome analysis (ACA) map.
Supplementary files format and content: bedpe: chromatin loops
Supplementary files format and content: bedgraph: A/B compartment annotations
Supplementary files format and content: sw: HDF5-based file for storing 3D structure ensembles
Supplementary files format and content: assembly: text file describing the relationship between the draft assembly and the chromosome-length upgrade
Supplementary files format and content: bed: gene annotations

organism: Elephas maximus indicus

source_name: blood: Ear vein

extract_protocol:
The protocol is described in detail in Sandoval-Velasco, Dudchenko, Rodríguez, Pérez Estrada et al., 2024. Briefly, PaleoHi-C is a a modified in situ Hi-C protocol, tailored towards working with highly degraded samples. The principal modifications were: (i) immediate preservation in the field using ethanol to reduce microbial activity; and (ii) sequestration of chromatin bodies on beads; (iii) removal of shearing and size selection given the lack of high molecular weight DNA; and (iv) library amplification using a paleo-compatible workflow
Library contruction protocol is described in detail in Sandoval-Velasco, Dudchenko, Rodríguez, Pérez Estrada et al., 2024.
Modified Hi-C.

value: blood:Ear vein


title: DC061DX


title: JN-DSRCT-1, siEWSR1::WT1, R2, ATAC

city: Villejuif

first: Clémence

last: Henon

address: 114 rue Edouard Vaillant

institute: Gustave Roussy

data_processing:
ATAC-seq data were analyzed according to nf-core/atacseq pipeline
Raw reads quality control (QC) was performed using FastQC
Adapter trimming was done with Trim Galore!
Read mapping to the reference genome (GRCh38) was done using BWA
Duplicate reads were discarded using picard
BigWig files were generated using BEDTools for IGV visualization
Assembly: GRCh38
Supplementary files format and content: BigWig files

growth_protocol: JN-DSRCT-1 cell line was maintained in 2D adherent culture within DMEM/F-12 (GibcoTM) supplemented with 10% FBS, 1% Penicillin-Streptomycin (GibcoTM), 1% Sodium Pyruvate (GibcoTM), 1% Sodium Bicarbonate (GibcoTM), 1% Non-Essential Amino Acids (GibcoTM) and 1% HEPES (GibcoTM). Cell passaging was performed at 1/10 twice a week. Used cells were controlled for mycoplasma-free status.

extract_protocol:
ATAC was performed according to Omni-ATAC protocol (Corces et al., Nat Methods, 2017). DNA purification was then performed using the Qiagen MinElute Reaction Cleanup kit.
NebNextUltra II Library prep kit for DNA

treatment_protocol: JN-DSRCT-1 cell line was transfected with a custom siRNA targeting EWSR1::WT1 (3’ GAT CTT GAT CTA GGT GAG A 5’), CCND1 (Horizon Discovery «on»-TARGETplus Human CCND1 siRNA-smart pool, reference L-003210–00-0005) or non-targeting siRNA (Horizon Discovery «on»-TARGETplus Non-targeting siRNA#1, reference D-001810-01-05), according to manufacturer’s instructions. After cell seeding and obtention of 50% confluency, transfection was performed using LipofectamineTM RNAiMAX (InvitrogenTM reference 13778150), and the medium was replaced the day after. A 48-hour silencing time point was used for each described experiment.

value: Desmoplastic Small Round Cell Tumor

value: EWSR1::WT1-targeting siRNA


title: JN-DSRCT-1, siCCND1, R1, ATAC

value: CCND1-targeting siRNA


title: JN-DSRCT-1, siCTRL, R1, ATAC

value: control non-targeting siRNA


title: JN-DSRCT-1, no_si, R2, ATAC

value: no siRNA


title: JN-DSRCT-1, siCTRL, R2, ATAC


title: JN-DSRCT-1, no_si, R1, ATAC


title: Brain_Control_12 days_2

value: Female


title: IC1, Visium

description:
FFPE Spatial transcriptome sequencing
Patient raw data cannot be provided due to privacy concerns

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to GRCh38 using Space Ranger's default settings
Gene expression level of Refseq coding genes were quantified using Space Ranger's default settings
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Echange Format
Supplementary files format and content: aligned_fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz: scale factors in json format
Supplementary files format and content: tissue_hires_image.png.gz: high-resolution image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz: low-resolution image of tissue
Supplementary files format and content: tissue_positions_list.csv.gz: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial transcriptomics

source_name: Desmoplastic Small Round Cell Tumor

extract_protocol:
We used five-mm sections of selected areas from scRNA-seq-matched FFPE samples. Extraction, whole transcriptome probe hybridization, release, and capture were performed according to Visium Spatial Gene expression for FFPE samples standard protocol.
Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's protocol


title: JN-DSRCT-1, siCCND1, R2, ATAC


title: GR7_site2, Visium


title: GR4, Visium


title: GR4_PC, Visium


title: heso1-4_rep2

description: sRNAseq libraries

value: inflorescences


title: Western ringtail possum (Sample1780)

organism: Pseudocheirus occidentalis


title: P29

description:
Count matrix in transcript per million for all RNA-seq samples (N=29: GR129T01, GR111T01, GR130T01, GR131T01, GR113T01, GR114T01, GR133T01, GR115T01, GR116T01, GR117T01, GR134T01, GR118T01, GR119T01, GR120T01, GR121T01, GR122T01, GR135T01, GR123T01, GR124T01, GR125T01, GR136T01, GR128T01, GR108T01, GR109T01, GR110T01, GR101T01, GR103T01, GR106T01, GR107T01)
Patient raw data cannot be provided due to privacy concerns

data_processing:
RNA-seq data were analyzed according to nf-core/rnaseq pipeline
Raw reads quality control (QC) was performed using FastQC
Adapter trimming was done with Trim Galore!
Alignment to the reference genome and transcript quatification were performed using Salmon
Assembly: hg19 (GENCODE version 19)
Supplementary files format and content: Count matrix in transcript per million

source_name: DSRCT, frozen tumor samples, RNA-seq

extract_protocol:
Ribbon sections of frozen samples were cut using a cryostat microtome after embedding within O.C.T. Next, frozen tissue was lyzed using Qiagen TissueLyser II with 3 mm tungsten carbide beads according to manufacturer protocol. RNA extraction was then performed using the Qiagen AllPrep DNA/RNA kit standard protocol.
After the QC procedure, rRNA was removed using the Ribo-Zero kit that leaves the mRNA. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs(dUTP, dATP, dGTP and dCTP), RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Then followed by purification by AMPure XP beads, terminal repair, polyadenylation, sequencing adapter ligation, size selection and degradation of second-strand U-contained cDNA by the USER enzyme. The strand-specific cDNA library was generated after the final PCR enrichment.

tag: patient id

tag: sample id

tag: ewsr1 breakpoint_exon

tag: wt1 breakpoint_exon

tag: sampling site

value: Testis

tag: age

value: M

tag: deceased

tag: follow-up duration_(months)

tag: prior chemotherapy

tag: number of_prior_chemotherapy_lines

tag: chemotherapy regimens

value: L1:IVA/AI, L2:VIP


title: P27

tag: tissue

value: Thorax wall


title: GR11_site1, Visium


title: P26

value: Peritoneum


title: GR2_site4, Visium


title: P23

value: L1:AI, L2:VAC


title: P24


title: Hi-C of Elephas maximus DNA Zoo Sample0045, part3

description:
ASM1433276v1.hic
ASM1433276v1_HiC.fasta.gz
ASM1433276v1.rawchrom.hic
EM_pbmc_Loxafr3.0_HiC.hic
EM_pbmc_Loxafr3.0_HiC_30.hic
EM_pbmc_MamPri_Loxafr3.0_assisted_HiC.hic
EM_pbmc_MamPri_Loxafr3.0_assisted_HiC_30.hic
EM_pbmc_MamPri_ASM1433276v1_assisted_HiC.hic
EM_pbmc_MamPri_ASM1433276v1_assisted_HiC_30.hic
HIC1382_ASM1433276v1_HiC.hic
HIC1382_ASM1433276v1_HiC_30.hic


title: P22


title: Brain_20Gy_ 24 hours_1

value: Brain

value: 24 hours


title: Hi-C of Elephas maximus DNA Zoo Sample0045, part1


title: JN-DSRCT-1, siEWSR1::WT1, R1, ATAC

tag: cell line

tag: cell type

tag: treatment


title: P20

tag: gender


title: P19

value: L1:AI followed by HIPEC, post-operative VAC, L2:pazopanib


title: P15


title: P17


title: P16

value: L1:IVADo/IVA followed by Carboplatin-Thiotepa


title: P14

value: Desmoplastic Small Round Cell Tumor


title: P18


title: P13


title: P12

value: F


title: P10


title: P5

value: L1:IVADO/IVA followed by TEMIRI


title: P7


title: P4


title: P8


title: P6


title: P25


title: P1

value: Ovary


title: P3


title: JN-DSRCT-1, siEWSR1::WT1, R2, RNA-seq

description: column H48_sifusion_R2

data_processing:
RNA-seq data were analyzed according to nf-core/rnaseq pipeline
Raw reads quality control (QC) was performed using FastQC
Adapter trimming was done with Trim Galore!
Pseudoalignment to the reference genome and transcript quatification were performed using Salmon
Assembly: hg19 (GENCODE version 19)
Supplementary files format and content: Count matrix in transcript per million

extract_protocol:
Cells were collected at 4°C in PBS after 48-hour silencing. Cell pellets were lyzed and RNA extracted using Qiagen RNEasy kit according to manufacturer's instructions. RNA quality control was performed before library construction based on RNA Integrity Number (RIN) evaluated on Agilent 2100 Bioanalyzer.
After the QC procedure, rRNA was removed using the Ribo-Zero kit that leaves the mRNA. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs(dUTP, dATP, dGTP and dCTP), RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Then followed by purification by AMPure XP beads, terminal repair, polyadenylation, sequencing adapter ligation, size selection and degradation of second-strand U-contained cDNA by the USER enzyme. The strand-specific cDNA library was generated after the final PCR enrichment.

treatment_protocol: JN-DSRCT-1 cell line was transfected with a custom siRNA targeting EWSR1::WT1 (3’ GAT CTT GAT CTA GGT GAG A 5’) or non-targeting siRNA (Horizon Discovery «on»-TARGETplus Non-targeting siRNA#1, reference D-001810-01-05), according to manufacturer’s instructions. After cell seeding and obtention of 50% confluency, transfection was performed using LipofectamineTM RNAiMAX (InvitrogenTM reference 13778150), and the medium was replaced the day after. A 48-hour silencing time point was used for each described experiment. The experiment was performed in triplicate.

value: EWSR1::WT1-targeting siRNA


title: P28


title: JN-DSRCT-1, siEWSR1::WT1, R3, RNA-seq

description: column H48_sifusion_R3


title: P21


title: JN-DSRCT-1, siCTRL, R3, RNA-seq

description: column H48_siCTRL_R3

value: control non-targeting siRNA


title: JN-DSRCT-1, siCTRL, R2, RNA-seq

description: column H48_siCTRL_R2


title: JN-DSRCT-1, siEWSR1::WT1, R1, RNA-seq

description: column H48_sifusion_R1


title: JN-DSRCT-1, siCTRL, R1, RNA-seq

description: column H48_siCTRL_R1


title: JN-DSRCT, assay_2, siCTRL, H3K9ac, ChIP-seq

data_processing:
ChIP-seq data analyses were performed according to nf-core/chipseq pipeline
Raw reads quality control (QC) was performed using FastQC
Adapter trimming was done with Trim Galore!
Reads were further mapped to the reference genome (GRCh38) using BWA
Duplicate reads were discarded using picard
BigWig files were generated using BEDTools to allow IGV visualization of fragments
Assembly: GRCh38
Supplementary files format and content: BigWig files

growth_protocol: JN-DSRCT-1 cell line was maintained in 2D adherent culture within DMEM/F-12 (GibcoTM) supplemented with 10% FBS, 1% Penicillin-Streptomycin (GibcoTM), 1% Sodium Pyruvate (GibcoTM), 1% Sodium Bicarbonate (GibcoTM), 1% Non-Essential Amino Acids (GibcoTM) and 1% HEPES (GibcoTM). Cell passaging was performed at 1/10 twice a week. Used cells were controlled for mycoplasma-free status. For ChIP assay, JN-DSRCT-1 cells were grown to ~80% confluence in 15 cm dishes.

extract_protocol:
Chromatin was crosslinked for 15 minutes at room temperature (RT) by adding methanol-free formaldehyde (1% final) in the dishes culture media. Then, formaldehyde was quenched by adding a glycine solution, and cells were scraped and centrifuged before freezing for subsequent utilization. After thawing on ince, cells were resuspended in FL buffer before nuclei extraction according to the NEXSON protocol (Arrigoni et al., Nucleic Acids Res, 2016). Immunoprecipitation was performed on sheared chromatin using H3K9ac, H3K27ac, WT1 C-terminal (GTX15249), or rabbit isotype antibodies overnight and immune complexes were captured the next day using Dynabeads Protein G beads. Crosslink was reverted with Proteinase K and DNA was purified on Qiagen PCR purification columns.
NebNextUltra II Library prep kit for DNA

treatment_protocol: No treatment was performed on JN-DSRCT-1 cells for assay 1. For assay 2, JN-DSRCT-1 cell line was transfected with a custom siRNA targeting EWSR1::WT1 (3’ GAT CTT GAT CTA GGT GAG A 5’), or non-targeting siRNA (Horizon Discovery «on»-TARGETplus Non-targeting siRNA#1, reference D-001810-01-05), according to manufacturer’s instructions. After cell seeding and obtention of 50% confluency, transfection was performed using LipofectamineTM RNAiMAX (InvitrogenTM reference 13778150), and the medium was replaced the day after. A 48-hour silencing time point was used for each described experiment.


title: JN-DSRCT, assay_2, siEWS-WT1, H3K9ac, ChIP-seq


title: JN-DSRCT-1, assay_2, siEWS-WT1, input


title: JN-DSRCT, assay_2, siCTRL, H3K27ac, ChIP-seq


title: JN-DSRCT, assay_1, WT1, R2, ChIP-seq


title: P11


title: JN-DSRCT-1, assay_2, siCTRL, input


title: JN-DSRCT, assay_1, WT1, R1, ChIP-seq


title: P9


title: JN-DSRCT, assay_1, isotype, R2, ChIP-seq


title: JN-DSRCT, assay_1, isotype, R1, ChIP-seq


title: P2


title: JN-DSRCT-1, assay_1, input


title: JN-DSRCT, assay_2, siEWS-WT1, H3K27ac, ChIP-seq


title: blood_AA028_3 mnd

city: Amsterdam

first: Jelle

middle: Maarten

last: Blankestijn

address: meibergdreef 9

country: Netherlands

institute: Amsterdam UMC

data_processing:
Read quality of the paired-end reads was assessed using FastQC (version 0.12.1). Sequencing adapters, low quality reads and low quality read ends were removed using Trim Galore (version 0.10.6), which is a wrapper around Cutadapt (version 4.3) and FastQC. Mapping and read quantification was performed with Salmon (version 1.10.1), where the human GRCh38.p14 genome was used as a reference genome with annotation provided by Ensembl.
Assembly: GRCh38.p14
Supplementary files format and content: comma separated file containing the raw counts for each sample

extract_protocol:
The PAXGene Blood RNA kit (QIAGEN) was then followed for RNA isolation according to protocol
Library prep was performed using the KAPA hyperPrep kit (Roche) according to protocol

value: blood

tag: time

value: 3 mnd

tag: genotype

value: WT

value: No treatment


title: blood_AV016_3 mnd


title: blood_AA018_12 mnd

value: 12 mnd


title: blood_HS021_3 mnd


title: blood_HS005_12 mnd


title: blood_HS001_3 mnd


title: blood_HS006_12 mnd


title: blood_AA032_3 mnd


title: blood_HS004_12 mnd


title: blood_LL001_12 mnd


title: blood_AA014_12 mnd


title: blood_AA029_3 mnd


title: blood_AV002_12 mnd


title: blood_AA030_3 mnd


title: blood_AV017_3 mnd


title: blood_HS020_3 mnd


title: blood_AA027_3 mnd


title: blood_AA026_3 mnd


title: blood_AV014_3 mnd


title: blood_AV013_3 mnd


title: blood_AV015_3 mnd


title: blood_AA024_3 mnd


title: blood_AA015_12 mnd


title: blood_AV012_3 mnd


title: blood_AA025_3 mnd


title: blood_HS022_3 mnd


title: blood_AA017_12 mnd


title: blood_HS003_12 mnd


title: blood_AA009_3 mnd


title: blood_AA016_12 mnd


title: blood_AV010_3 mnd


title: blood_HS015_3 mnd


title: blood_HS014_3 mnd


title: blood_HS012_3 mnd


title: blood_HS016_3 mnd


title: blood_LL009_3 mnd


title: blood_AA008_12 mnd


title: blood_AA013_12 mnd


title: blood_HS002_12 mnd


title: blood_HS019_3 mnd


title: blood_HS018_3 mnd


title: blood_AV011_3 mnd


title: blood_HS013_3 mnd


title: blood_HS001_12 mnd


title: blood_AA007_3 mnd


title: blood_AA007_12 mnd


title: blood_HS017_3 mnd


title: blood_AA010_12 mnd


title: blood_AV009_3 mnd


title: blood_HS011_3 mnd


title: blood_AA006_3 mnd


title: blood_AA002_12 mnd


title: blood_AA023_3 mnd


title: blood_AV005_3 mnd


title: blood_HS010_3 mnd


title: blood_AV008_12 mnd


title: blood_AA021_3 mnd


title: blood_AV006_3 mnd


title: blood_AA022_3 mnd


title: blood_HS009_3 mnd


title: blood_AV004_3 mnd


title: blood_HS008_3 mnd


title: blood_LL005_3 mnd


title: blood_LL004_3 mnd


title: blood_LL003_3 mnd


title: blood_AA016_3 mnd


title: blood_LL006_3 mnd


title: blood_AA020_3 mnd


title: blood_HS003_3 mnd


title: blood_AA005_3 mnd


title: blood_HS006_3 mnd


title: blood_VV010_12 mnd


title: blood_HS007_12 mnd


title: blood_LL002_12 mnd


title: blood_AA019_3 mnd


title: blood_AA015_3 mnd


title: blood_AA017_3 mnd


title: blood_HS004_3 mnd


title: blood_HS007_3 mnd


title: blood_VV007_12 mnd


title: blood_LL002_3 mnd


title: blood_VV009_12 mnd


title: blood_AA012_3 mnd


title: blood_VV006_12 mnd


title: blood_VV011_12 mnd


title: blood_AA014_3 mnd


title: blood_VV008_12 mnd


title: blood_HS002_3 mnd


title: blood_AV003_3 mnd


title: blood_AA003_3 mnd


title: blood_VV005_12 mnd


title: blood_VV002_12 mnd


title: blood_VV001_12 mnd


title: blood_AA019_12 mnd


title: blood_VV004_3 mnd


title: blood_AA011_3 mnd


title: blood_VV012_3 mnd


title: blood_VV010_3 mnd


title: blood_VV007_3 mnd


title: blood_VV008_3 mnd


title: blood_VV011_3 mnd


title: blood_VV013_3 mnd


title: PREDICATE_100

first: Louis

last: Vermeulen

address: Meibergdreef 9

department: LEXOR Department

institute: Amsterdam University Medical Center

data_processing:
RNA-seq raw reads were mapped to the UCSC human reference genome (GRCh38) and calculation of gene counts using STAR (version 2.7.2b) with default parameters.
The multi-mapped reads were filtered out and only the uniquely mapped reads were retained.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: Metastatic colorectal cancer

growth_protocol: FFPE samples

extract_protocol:
Total RNA was extracted using AllPrep DNA/RNA FFPE isolation kit (Qiagen, Hilden, Germany) on the QIAcube classic ((cat. no. 9001293, Qiagen, Hilden, Germany). A total of 10ng of total RNA was used as input for RNA-seq per sample.
RNA libraries for RNA-seq were prepared using SMARTer Stranded Total RNA-sSeq Kit v3 – Pico from TakaraBio, Kusatsu, Japan.
RNA-seq, paired-end, 100M reads

treatment_protocol: No treatments applied on samples

value: Metastatic colorectal cancer

value: Anti-EGFR


title: PREDICATE_101


title: PREDICATE_104


title: PREDICATE_102


title: blood_VV002_3 mnd


title: blood_VV009_3 mnd


title: blood_AA020_12 mnd


title: blood_VV001_3 mnd


title: blood_AA010_3 mnd


title: PREDICATE_99


title: PREDICATE_103


title: PREDICATE_96


title: blood_VV003_3 mnd


title: blood_AA002_3 mnd


title: PREDICATE_97


title: PREDICATE_94


title: blood_VV005_3 mnd


title: PREDICATE_93


title: PREDICATE_92


title: PREDICATE_98


title: PREDICATE_88


title: PREDICATE_91


title: PREDICATE_87


title: PREDICATE_90


title: PREDICATE_86


title: PREDICATE_84


title: PREDICATE_85


title: PREDICATE_82


title: PREDICATE_83


title: PREDICATE_80


title: PREDICATE_78


title: PREDICATE_77


title: PREDICATE_79


title: PREDICATE_76


title: PREDICATE_81


title: PREDICATE_73


title: PREDICATE_75


title: PREDICATE_95


title: PREDICATE_71


title: PREDICATE_72


title: PREDICATE_69


title: PREDICATE_70


title: PREDICATE_67


title: PREDICATE_68


title: PREDICATE_66


title: PREDICATE_64


title: PREDICATE_89


title: PREDICATE_65


title: PREDICATE_59


title: PREDICATE_62


title: PREDICATE_61


title: PREDICATE_60


title: PREDICATE_58


title: PREDICATE_57


title: PREDICATE_74


title: PREDICATE_53


title: PREDICATE_56


title: PREDICATE_51


title: PREDICATE_52


title: PREDICATE_49


title: PREDICATE_50


title: PREDICATE_46


title: PREDICATE_44


title: PREDICATE_45


title: PREDICATE_43


title: PREDICATE_42


title: PREDICATE_40


title: PREDICATE_39


title: PREDICATE_41


title: PREDICATE_38


title: PREDICATE_63


title: PREDICATE_37


title: PREDICATE_36


title: PREDICATE_55


title: PREDICATE_35


title: PREDICATE_34


title: PREDICATE_30


title: PREDICATE_33


title: PREDICATE_54


title: PREDICATE_32


title: PREDICATE_29


title: PREDICATE_48


title: PREDICATE_27


title: PREDICATE_26


title: PREDICATE_28


title: PREDICATE_25


title: PREDICATE_47


title: PREDICATE_22


title: PREDICATE_21


title: PREDICATE_20


title: PREDICATE_19


title: PREDICATE_18


title: PREDICATE_17


title: PREDICATE_16


title: PREDICATE_15


title: PREDICATE_14


title: PREDICATE_31


title: PREDICATE_12


title: PREDICATE_13


title: PREDICATE_10


title: PREDICATE_9


title: PREDICATE_8


title: PREDICATE_7


title: PREDICATE_6


title: PREDICATE_4


title: PREDICATE_3


title: PREDICATE_2


title: PREDICATE_5


title: PREDICATE_24


title: PREDICATE_1


title: PREDICATE_23


title: HiPSC-SNs expressing 3.2NP, repeat 3

city: Milwaukee

first: Hongwei

last: Yu

state: WI

address: 8701 Watertown plank Road

department: Anesthesiology

institute: Medical College of Wisconsin

data_processing:
Sequencing reads were aligned to the human GRCh38.p13 (Ensemble) transcriptome and processed through the MAPR-Seq Workflow with differential expression analysis completed using Bioconductor, edgeR v 3.8.6 software.
Genes with a false discovery rate (FDR) <0.05 and an absolute log2 fold change (log2FC)≥ 1 were initially filtered and considered significantly differentially expressed.
Assembly: GRCh38.p13
Supplementary files format and content: GeneCount.xlsx, contains raw and normalized counts for all individual samples for all genes.
Supplementary files format and content: SigDEgene_pairwise.xlsx, contains log fold change and false discovery rate statistic for each pairwise comparison, and raw counts for individual samples

source_name: Human iPSC-derived sensory neurons

growth_protocol: Human iPSC-derived sensory neurons were cultured in ChronoTM Senso-MM complete growth medium and medium changed very three days

extract_protocol:
Qiagen RNeasy
Illumina stranded total RNA, 500ng starting input (depending on quality and quantity of RNA).
Final assessment, quantification, and pooling of the RNAseq libraries were completed with qPCR (Kapa Library Quantification Kit, Kapa Biosystems) and DNA high sensitivity fragment analysis (Agilent).

treatment_protocol: At the 21 days of culture, hiPSC-SNs were transduced using lentivector-3.2iPA (treatment) and lentivector-3.2NP (control), respectively, for two days at multiplicity of infection=5. At the 28 days, the hiPSN-SNs were washed in PBS, collected, and pelleted by  centrifugation at 1500rpm for 5 minutes. Cell pelletes were stored in -80C untill RNAseq analysis.

value: Human iPSC-derived sensory neurons

value: Lentivector-3.2NP transductuion


title: HiPSC-SNs expressing 3.2NP, repeat 4


title: HiPSC-SNs expressing 3.2iPA, repeat 2

value: Lentivector-3.2iPA transductuion


title: HiPSC-SNs expressing 3.2iPA, repeat 1


title: HiPSC-SNs expressing 3.2iPA, repeat 4


title: HiPSC-SNs expressing 3.2NP, repeat 2


title: HiPSC-SNs expressing 3.2NP, repeat 1


title: HiPSC-SNs expressing 3.2iPA, repeat 3


title: PREDICATE_11


title: DC009

city: Los Angeles

first: Lihong

last: Huo

state: CA

address: 8700 Beverly Blvd, Los Angeles, CA 90048

institute: Cedars-Sinai

data_processing:
Raw reads obtained from RNA-Seq were aligned to the transcriptome using STAR (version 2.5.0) /RSEM (version 1.2.25) with default parameters, using a custom human GRCh38 transcriptome reference downloaded from https://www.gencodegenes.org, containing all protein coding and long non-coding RNA genes based on human GENCODE version 33 annotation.
Aligned reads were sorted and indexed using samtools v 1.18
Assembly: GRCh38
Supplementary files format and content: Comma separated value file containing raw read counts per sample per gene

source_name: whole blood

extract_protocol:
Blood samples were kept in PAXgene RNA tubes in -80 until ready to process. RNA was isolated using the PAXgene Blood RNA kit according to the manufacturers guidelines (PreAnalytiX). Eluted RNA was dissolved in RNase-free water. The quality and quantity of RNA were evaluated using the Agilent 2100 BioAnalyzer (Santa Clara, CA, USA).
Three hundred ng of total RNA Total was ribodepleted using the RiboCop Depletion Kit Human/Mouse/Rat v2 (Lexogen Inc., Greenland, NH).  Stranded RNA-Seq library construction was performed using the xGen Broad-Range RNA Library Prep Kit (Integrated DNA Technologies, Coralville, IA).  Library concentration was measured with a Qubit fluorometer (ThermoFisher Scientific), and library size was evaluated on a 4200 TapeStation (Agilent Technologies). Multiplexed libraries were sequenced on a NovaSeq 6000 (Illumina, San Diego, CA) using 75bp single-end sequencing. On average, approximately 50 million reads were generated from each sample.

value: whole blood

tag: disease state

value: healthy control


title: DC015


title: blood_VV006_3 mnd


title: OCI-AML3 cells, Nt_FLAG-HA-FKBP12(F36V)_DCAF15, DMSO (Control), rep1

city: Philadelphia

first: Luca

last: Busino

state: Pennsylvania

address: 421 Curie Boulevard

department: Cancer Biology

institute: University of Pennsylvania

data_processing:
Reads were mapped and analyzed with a bioinformatic pipeline based on STAR, SAMTOOLS, and the R package DESeq2
Assembly: GRCh38
Supplementary files format and content: normalized_OCI-AML3_counts.csv: csv file includes normalized counts for each OCI-AML3 Sample

growth_protocol: OCI-AML3 human acute myeloid leukemia cells were maintained in RPMI-1640 media supplemented with 10% fetal bovine serum (FBS) and 1% Penicillin/Streptomycin in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted from OCI-AML3 cells using the RNeasy Mini Kit (QIAGEN, 74104) per the manufacturer's instructions
Total RNA was shipped to GENEWIZ (Azenta Life Sciences) for Standard RNA-Seq service, where polyA+ transcripts were isolated and RNA-seq library was prepared per their in-house protocols

treatment_protocol:
Prior to experiment, OCI-AML3 cells were engineered with the FLAG-HA-FKBP12(F36V) tag (dTAG) knocked-in at the start codon of the endogenous DCAF15 genomic locus
Additionally, prior to experiment, OCI-AML3 Nt_FLAG-HA-FKBP12(F36V)_DCAF15 cells were single-cell cloned, and validated for homozygosity and dTAGv1 drug-induced degradation of endogenous DCAF15 protein
Cells were treated with DMSO, 250nM dTAGv1 drug for 24h, or 250nM dTAGv1 drug for 72h
At the end of the treatment time, cells were harvested and frozen for RNA extraction

value: acute myeloid leukemia

value: DMSO


title: OCI-AML3 cells, Nt_FLAG-HA-FKBP12(F36V)_DCAF15, dTAGv1_72h, rep2


title: OCI-AML3 cells, Nt_FLAG-HA-FKBP12(F36V)_DCAF15, dTAGv1_24h, rep3


title: OCI-AML3 cells, Nt_FLAG-HA-FKBP12(F36V)_DCAF15, dTAGv1_24h, rep1


title: OCI-AML3 cells, Nt_FLAG-HA-FKBP12(F36V)_DCAF15, DMSO (Control), rep2


title: OCI-AML3 cells, Nt_FLAG-HA-FKBP12(F36V)_DCAF15, dTAGv1_24h, rep2


title: OCI-AML3 cells, Nt_FLAG-HA-FKBP12(F36V)_DCAF15, dTAGv1_72h, rep1


title: OCI-AML3 cells, Nt_FLAG-HA-FKBP12(F36V)_DCAF15, dTAGv1_72h, rep3


title: DC013


title: OCI-AML3 cells, Nt_FLAG-HA-FKBP12(F36V)_DCAF15, DMSO (Control), rep3


title: DC012


title: DC006


title: DC007


title: DP002

value: SLE CMD


title: DC002


title: DP015

value: SLE non-CMD


title: DP001


title: DP009


title: DP012


title: DC008


title: DP006


title: DP007


title: DP008


title: DP005


title: DC014


title: DC010


title: LX-2_siOGT_rep1

city: Lille

first: Jérôme

last: Eeckhoute

address: Bâtiment J&K, Faculté de Médecine de Lille-Pôle Recherche, Boulevard du Professeur Leclerc

institute: CNRS

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using  SOAPnuke
Mapping of reads to the human genome (hg38) was achieved using Bowtie2 (v2.3.5.1; parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200) using the GENCODE annotation GRCh38.84
Read counting was then performed using the RNA‑Seq by Expectation Maximization (RSEM, v1.3.1; parameters: -p 8 --forward-prob 0 --paired-end)
Normalization and differential gene expression analyses were performed using DESeq2 (v1.36.0). Genes with low expression (total read counts below 10) were removed and treatment and control samples from the same replicate were paired for differential expression analysis.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include Ensembl IDs and count values for each Sample
Supplementary files format and content: Matrix table include normalized abundance measurements (output from DESeq2 ; "sign_siOGT_control_genes_with_Batch_all.csv" file)

growth_protocol: LX-2 cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM, GibcoTM) supplemented with 5% fetal bovine serum (FBS, Deutscher).

extract_protocol:
LX-2 total RNA was harvested using Nucleospin® RNA kit (Macherey-Nagel).
RNA libraries for RNA-seq were prepared with DNBSEQ stranded mRNA library after oligo dT based enrichment

treatment_protocol: LX-2 cells were transfected with siControl or siOGT at 20 nM for 72 h using JetPrime® (Polyplus transfection) (3 biological replicates)

value: Hepatic Stellate Cells

value: siOGT


title: LX-2_siOGT_rep3


title: LX-2_siControl_rep2

value: siControl


title: LX-2_siOGT_rep2


title: LX-2_TEAD4_ChIPseq_rep3

data_processing:
After initial quality controls of fastq files, raw data were mapped to hg38 using Chromap (v0.1.3-R256) and the following parameters: error threshold: 8, min-num-seeds: 2, max-‑seed-‑frequency: 500,1000, max-num-best-mappings: 1, max-insert-size: 1000, MAPQ‑threshold: 10, min-read-length: 30, bc-error-threshold: 1, bc-probability-threshold: 0.90.
Bam files for TEAD4 ChIP-seq data (n=3 biological replicates) were analyzed using the Irreproducible Discovery Rate (IDR), which allows to identify TF binding peaks that are reproducible and rank-concordant across replicates (Ref). This was performed using the IDR pipeline from ENCODE version 2.2.1 installed from https://github.com/ENCODE-DCC/chip-seq-pipeline2/tree/master (Ref). IDR identified that only 2 replicates were concordant enough (replicates 1 and 3), which were therefore used to re-run IDR and identify TEAD4 binding peaks and obtain a TEAD4 ChIP-seq signal track
Assembly: hg38
Supplementary files format and content: IDR identified TEAD4 peaks (bed file)
Supplementary files format and content: TEAD4 IDR issued average fold enrichment over input (bigwig file)

extract_protocol:
Cells were crosslinked for 10 min at room temperature with 1% formaldehyde (FA). Samples were processed as in Dubois V. et al Mol Syst Biol 2020.
DNBseq sequencing was performed; read Length: SE50


title: DP010


title: LX-2_siControl_rep1


title: LX-2_Input_ChIPseq_rep3


title: LX-2_TEAD4_ChIPseq_rep2


title: LX-2_TEAD4_ChIPseq_rep1


title: Rest_D440_Day_0_ATAC

city: New York

first: Bikash

last: Mishra

address: 515 E 71st ST

institute: Hospital for Special Surgery

data_processing:
Raw data underwent adapter trimming with FastP.
Sequencing read alignments were performed against (GRCh38/hg38) reference human genome using Bowtie2.
Peak calling was performed using MACS3 with the following parameters: "macs3 callpeak -f BAMPE -t sample_name -g hs -q 0.01 --keep-dup 1000 --nomodel --shift 0 --extsize 150".
Peaks present in all 3 replicates are taken for downstream analysis
Assembly: hg38
Supplementary files format and content: BED file includes union peak used to run TOBIAS analysis
Supplementary files format and content: Tab-delimited text files include log2CPM values for each sample

source_name: CD14+ monocytes

growth_protocol: Peripheral blood mononuclear cells were obtained from the blood of healthy donors by density gradient centrifugation using Ficoll (Invitrogen) and a protocol approved by the Hospital for Special Surgery Institutional Review Board. CD14+ human monocytes were purified from PBMCs by positive selection using anti-CD14 magnetic beads as recommended by the manufacturer (Miltenyi Biotec). Monocytes were cultured in Roswell Park Memorial Institute (RPMI) 1640 medium (Invitrogen) supplemented with 10% heat-inactivated defined FBS (HyClone), penicillin/streptomycin (Invitrogen), L-glutamine (Invitrogen), and 20 ng/mL human macrophage colony-stimulating factor (M-CSF; Peprotech).

extract_protocol:
Cells were lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Immediately after lysis, nuclei were spun at 500 x g for 10 min in a refrigerated centrifuge. Immediately following the nuclei prep, the pellet was resuspended in the transposase reaction mix (25 µl 2× TD buffer, 2.5 µl transposase (Illumina) and 22.5 µl nuclease-free water). The transposition reaction was carried out for 30 min at 37 °C. Directly following transposition, the sample was purified using a MinElute PCR Purification kit.
Library fragments were amplified using 1× NEB next PCR master mix and 1.25 M of custom Nextera PCR primers as previously described, sing the following PCR conditions: 72 °C for 5 min; 98 °C for 30 s; and thermocycling at 98 °C for 10 s, 63 °C for 30 s and 72 °C for 1 min. The libraries were purified using a Qiagen PCR cleanup kit yielding a final library concentration of ∼30 nM in 20 µl.

treatment_protocol: Human CD14+ monocytes were cultured in M-CSF (20ng/ml) with or without IFNg (100 Units/ml) overnight and then stimulated with LPS (10 ng/ml, for 3 hours), MonoMacs were cultured for 72hours in M-CSF and stimulated similarly to monocytes.

value: CD14+ monocytes

value: Resting (Control)


title: Rest_D440_Day_3_ATAC


title: LPS_D440_Day_0_ATAC

value: LPS


title: LPS_D440_Day_3_ATAC


title: Rest_D442_Day_0_ATAC


title: LPS_D442_Day_3_ATAC


title: LPS_D441_Day_3_ATAC


title: DP004


title: Rest_D441_Day_3_ATAC


title: LPS_D441_Day_0_ATAC


title: LX-2_OSMI-1_CoPseq

data_processing:
After initial quality controls of fastq files, raw data were mapped to hg38 using Chromap (v0.1.3-R256) and the following parameters: error threshold: 8, min-num-seeds: 2, max-‑seed-‑frequency: 500,1000, max-num-best-mappings: 1, max-insert-size: 1000, MAPQ‑threshold: 10, min-read-length: 30, bc-error-threshold: 1, bc-probability-threshold: 0.90.
Bam files for H3K27ac ChIP-seq data were next used for peak calling in each replicate using model-based analysis of ChIP-seq version 2 (MACS2 v2.1.1.20160309) in a local instance of Galaxy. Input DNA was used as control (inputs from either DMSO or OSMI-1 treated cells were merged for these analyses), duplicated reads were removed together with those mapping to ENCODE Blacklisted regions (v2). Parameters used were: Band width for picking regions to compute fragment size: 300, Set lower mfold bound: 5, Set upper mfold bound: 50, Peak detection based on: qvalue, Minimum false discovery rate (FDR q-value) cutoff for peak detection: 0.05, Build Model: nomodel, Set extension size: 200, Set shift size: 0. Bam files and bed files issued from the peak calling analyses of the 8 datasets were used for data normalization and identification of regions with differential H3K27ac enrichment between OSMI-1-treated and control cells using MAnorm2. To get signal tracks of normalized H3K27ac ChIP-seq data, normalization coefficients defined by MAnorm2 were retrieved and applied to original Bam files. Average normalized signal tracks for H3K27ac ChIP-seq in OSMI-1-treated and control cells using multiBigwigSummary of the deepTools (v2.0).
CoP-seq raw data and mapping to hg38 were performed similarly to the ChIP-seq data. Signal tracks were obtained using the bamCoverage function of the deepTools with the following parameters: -bs 25 --normalizeUsing CPM -e 200.
Assembly: hg38
Supplementary files format and content: H3K27ac ChIP-seq: MAnorm2 normalized signal tracks and regions with differential H3K27ac signal in OSMI-1 treated versus control non-treated cells (FDR<0.15)
Supplementary files format and content: CoP-seq: Counts per Million (CPM) signal tracks

extract_protocol:
Cells were crosslinked for 10 min at room temperature with 1% formaldehyde (FA) for ChIP and 2% FA for CoP. Samples for ChIP were processed as in Dubois V. et al Mol Syst Biol 2020 while samples for CoP were processed as in Zhang et al Epigenetics & Chromatin 2020.
DNBseq sequencing was performed; read Length: SE50

treatment_protocol: LX-2 cells were treated with vehicle (DMSO) or OSMI-1 at 50 µM for 24 h (4 biological replicates for H3K27ac ChIP-seq and 1 biological replicate for CoP-seq)


title: Rest_D441_Day_0_ATAC


title: LPS_D442_Day_0_ATAC


title: IFNg_LPS_D442_Day_3_ATAC

value: IFNg + LPS


title: IFNg_LPS_D442_Day_0_ATAC


title: Rest_D442_Day_3_ATAC


title: IFNg_LPS_D441_Day_3_ATAC


title: LX-2_siControl_rep3


title: LX-2_OSMI-1_Input_CoPseq


title: IFNg_LPS_D441_Day_0_ATAC


title: IFNg_LPS_D440_Day_3_ATAC


title: LX-2_OSMI-1_H3K27ac_ChIPseq_rep4


title: LX-2_Input_ChIPseq_rep1-2


title: LX-2_OSMI-1_Input_ChIPseq_rep4


title: IFNg_D440_Day_3_ATAC

value: IFNg


title: LX-2_Control_H3K27ac_ChIPseq_rep3


title: IFNg_D441_Day_0_ATAC


title: IFNg_D440_Day_0_ATAC


title: LX-2_Control_H3K27ac_ChIPseq_rep1


title: LX-2_OSMI-1_H3K27ac_ChIPseq_rep3


title: IFNg_D442_Day_0_ATAC


title: Rest_D442_Day_0_RNA

data_processing:
Read quality was assessed and adapters trimmed using FastQC and cutadapt.
Reads were then mapped to the human genome (hg38) and reads in exons were counted against Gencode v38 with STAR Aligner.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes filtered raw counts and log2 transformed counts for each sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1Ug of total RNA was used for the construction of sequencing libraries.
The NEBNext® Poly(A) mRNA Magnetic Isolation Module was used to enrich Poly(A) mRNA (input for library prep) following the manufacturer's protocol. RNA libraries were prepared for sequencing utilizing the NEBNext® Ultra™ II Directional RNA Library Prep kit (E7765L) according to the manufacturer's instructions.


title: LX-2_Control_CoPseq


title: IFNg_D441_Day_3_ATAC


title: LX-2_OSMI-1_H3K27ac_ChIPseq_rep1


title: LX-2_OSMI-1_Input_ChIPseq_rep1-2-3


title: IFNg_LPS_D440_Day_0_ATAC


title: LX-2_OSMI-1_H3K27ac_ChIPseq_rep2


title: Rest_D440_Day_3_RNA


title: LX-2_Control_Input_ChIPseq_rep1-2-3


title: LX-2_Control_Input_CoPseq


title: Rest_D440_Day_0_RNA


title: Rest_D441_Day_0_RNA


title: LX-2_Control_H3K27ac_ChIPseq_rep4


title: LX-2_OSMI-1_rep3

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using  SOAPnuke
Mapping of reads to the human genome (hg38) was achieved using Bowtie2 (v2.3.5.1; parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200) using the GENCODE annotation GRCh38.84
Read counting was then performed using the RNA‑Seq by Expectation Maximization (RSEM, v1.3.1; parameters: -p 8 --forward-prob 0 --paired-end)
Normalization and differential gene expression analyses were performed using DESeq2 (v1.36.0). Genes with low expression (total read counts below 10) were removed and treatment and control samples from the same replicate were paired for differential expression analysis.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include Ensembl IDs and count values for each Sample
Supplementary files format and content: Matrix table include normalized abundance measurements (output from DESeq2 ; "signOSMI_control_genes_with_Batch_all.csv" file)

treatment_protocol: LX-2 cells were treated with vehicle (DMSO) or OSMI-1 at 50 µM for 24 h (4 biological replicates)


title: IFNg_D442_Day_3_ATAC


title: LPS_D442_Day_3_RNA


title: LX-2_OSMI-1_rep2


title: LX-2_Control_Input_ChIPseq_rep4


title: Rest_D442_Day_3_RNA


title: LX-2_Control_H3K27ac_ChIPseq_rep2


title: LX-2_OSMI-1_rep4


title: Rest_D441_Day_3_RNA


title: LPS_D442_Day_0_RNA


title: LX-2_OSMI-1_rep1


title: LPS_D441_Day_3_RNA


title: LX-2_Control_rep4

value: DSMO


title: LX-2_Control_rep3


title: LPS_D441_Day_0_RNA


title: LPS_D440_Day_0_RNA


title: LPS_D440_Day_3_RNA


title: LX-2_Control_rep1


title: LX-2_Control_rep2


title: IFNg_LPS_D442_Day_0_RNA


title: MC1742 - 1

first: Mathieu

last: Gissot

address: 1, rue du Pr. calmette

data_processing:
Clusters were generated on a flow cell within a cBot using the Cluster Generation Kit (Illumina), and libraries were sequenced as 50-bp reads on a HiSeq 2500 using a Sequence By Synthesis (SBS) technique (Illumina).
Image analysis and base calling were performed using the HiSeq Control Software and Real-Time Analysis component. Demultiplexing was performed using Illumina’s conversion software (bcl2fastq 2.17). The quality of the data was assessed using FastQC from the Babraham Institute and the Illumina software Sequence Analysis Viewer (SAV). Potential contaminants were investigated with the FastQ Screen software from the Babraham Institute.
Datasets were aligned with HiSAT2 v2.1.0  against the T. gondii ME49 genome from (ToxoDB-39)  and to the rat genome (Rattus norvegicus Rn6 (UCSC)). Final read alignments having more than three mismatches were discarded. Gene counting was performed using HTSeq-count 0.6.1p1 (union mode). Because the data come from a strand-specific assay, the read must be mapped to the opposite strand of the gene. Before statistical analysis, genes with less than 15 reads (combining all the analyzed samples) were filtered out. Differentially expressed genes were identified using the Bioconductor package edgeR 3.6.7. The data were normalized using the Relative Log Expression (RLE) normalization factors. Genes with adjusted p-values less than 5% (according to the FDR method from Benjamini-Hochberg) were declared differentially expressed.
Genome_build: T. gondii ME49 genome from (ToxoDB-39)
Supplementary_files_format_and_content: DESeq2_MC1742.complete

organism: Toxoplasma gondii

source_name: Human fibroblast culture infected with T. gondii

growth_protocol: Intracellular parasite were grown for 24 hours and then submitted to 6 hours of treatment with DMSO or MC1742 (0.5 µM)

extract_protocol:
Total RNA was extrated using TRIzol reagent according to manufacturer’s protocol.
Library preparation was performed using the TruSeq Stranded mRNA Sample Preparation kit (Illumina) according to the manufacturer’s instructions. Libraries were validated using a Fragment Analyzer and quantified by qPCR (ROCHE LightCycler 480).

tag: strain

value: RH

value: 6 hours of treatment with MC1742 (0.5 µM)


title: MC1742 - 2


title: IFNg_LPS_D441_Day_0_RNA


title: MC1742 - 3


title: IFNg_LPS_D441_Day_3_RNA


title: IFNg_LPS_D440_Day_3_RNA


title: DMSO - 3

value: 6 hours of treatment with DMSO


title: DMSO - 2


title: IFNg_LPS_D440_Day_0_RNA


title: Hi-C of Equus asinus DNA Zoo Sample0158, rep2

description:
EquAsi_EquCab2.0_assisted_HiC.fasta.gz
EquAsi_EquCab2.0_assisted.hic
EquAsi_EquCab2.0_assisted.rawchrom.hic
ASM303372v1_HiC.fasta.gz
ASM303372v1_HiC.assembly
ASM303372v1.hic
ASM303372v1.rawchrom.hic

data_processing:
Hi-C-guided genome assembly (3D-DNA, JBAT)
Reference-guided 3D genome assembly (Anonamos, 3D-DNA, JBAT)
Construction of the chromosome-length Hi-C contact map (BWA, Juicer, 3D-DNA)
liftover (KentUtils, 3D-DNA)
Gene annotation (TOGA)
Compartment annotation (CRUSH)
Loop calling and aggregate analysis (HiCCUPS, Juicer Tools, SIP, SIP META)
Aggregate chromosome analysis (3D-DNA)
Modeling of 3D structures of woolly mammoth chromosomes (OpenMiChroM)
DNA degradation simulations (NuChroM, custom script)
Assembly: The following existing genome builds were used in parts of the study: Loxafr3.0 (GCA_000001905.1), ASM1433276v1 (GCA_014332765.1), EquCab2.0 (GCF_000002305.2), ASM303372v1 (GCA_003033725.1), bosTau9 (GCF_002263795.3), ASM651725v1 (GCF_006517255.1), ASM3043605v1 (GCF_030436055.1), ASM331443v2 (GCF_003314435.2), hg38, hg19.
Supplementary files format and content: fasta.gz: chromosome-length nucleotide sequences generated usign Hi-C-guided genome assembly
Supplementary files format and content: hic: contact maps generated by aligning Hi-C data to reference sequences. In addition to "standard" hic maps build against chromosome-length references included are "assembly" maps generated by 3D-DNA for before and after genome assembly and an aggregate chromosome analysis (ACA) map.
Supplementary files format and content: bedpe: chromatin loops
Supplementary files format and content: bedgraph: A/B compartment annotations
Supplementary files format and content: sw: HDF5-based file for storing 3D structure ensembles
Supplementary files format and content: assembly: text file describing the relationship between the draft assembly and the chromosome-length upgrade
Supplementary files format and content: bed: gene annotations

organism: Equus asinus

extract_protocol:
The protocol is described in detail in Sandoval-Velasco, Dudchenko, Rodríguez, Pérez Estrada et al., 2024. Briefly, PaleoHi-C is a a modified in situ Hi-C protocol, tailored towards working with highly degraded samples. The principal modifications were: (i) immediate preservation in the field using ethanol to reduce microbial activity; and (ii) sequestration of chromatin bodies on beads; (iii) removal of shearing and size selection given the lack of high molecular weight DNA; and (iv) library amplification using a paleo-compatible workflow
Library contruction protocol is described in detail in Sandoval-Velasco, Dudchenko, Rodríguez, Pérez Estrada et al., 2024.
Modified Hi-C.

value: blood


title: IFNg_D442_Day_0_RNA


title: Hi-C of Equus asinus DNA Zoo Sample0158, rep1


title: IFNg_D441_Day_3_RNA


title: DMSO - 1


title: IFNg_D442_Day_3_RNA


title: IFNg_LPS_D442_Day_3_RNA


title: Tumor-infiltrating immune cells, LNP-circRNACAR 2

city: Shenzhen

first: Chengzhi

last: Zhao

address: No. 1088 Xueyuan Avenue, Nanshan District, Shenzhen, Guangdong

institute: Southern University of Science and Technology

description:
treatment(LNP-circRNACAR)
GZ23100897

data_processing:
The raw FASTQ data underwent quality control analysis using FastQC
Trimmomatic was applied to filter out low-quality reads and trim adapter content, employing parameters LEADING:3, TRAILING:3, SLIDINGWINDOW:4:20, and MINLEN:36.
The filtered reads were aligned to the mouse reference genome (GRCm38) using HISAT2, followed by sorting of alignment results and storage in BAM format using SAMtools.
featureCounts was employed to generate the raw gene counts matrix, using parameters “-p --countReadPairs -t exon -g gene_id”.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw count for each Sample

extract_protocol:
Total RNA was extracted using the Quick-RNATM Miniprep Kit (ZYMO, # R1055)
RNA libraries for RNA-seq were prepared using the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina (New England Biolabs, #E7770S).

value: Tumor-infiltrating immune cells

value: LNP-circRNACAR treatment


title: IFNg_D440_Day_3_RNA


title: Tumor-infiltrating immune cells, LNP-circRNAEV 2

description:
treatment(LNP-circRNAEV)
GZ23100895

value: LNP-circRNAEV treatment


title: IFNg_D440_Day_0_RNA


title: IFNg_D441_Day_0_RNA


title: Tumor-infiltrating immune cells, LNP-circRNACAR 1

description:
treatment(LNP-circRNACAR)
GZ23100896


title: TN_P300_2

city: WORCESTER

first: Susu

last: Guo

state: MA

address: 7 Pocono Road

institute: UMASS Chan Medical School

data_processing:
Briefly, Fastp software (v0.20.0) was used to trim adaptor and remove low quality reads to get high quality clean reads. Clean reads were aligned to human hg38 reference genome using bowtie2 software (v2.2.4). Deeptools software (v3.5.1) was used to calculate and plot the correlations. MACS2 software (v2.2.7.1) was used for peak calling. ChIPSeeker R package (v1.30.3) was used for peak annotation. Homer software (v4.11) was used to identify motifs. MANorm2 softwre (v1.2.0) was used to identify differentially enriched regions between two samples and/or two groups of samples. The enriched peaks were visualized in IGV (v2.4.10) software. GO and KEGG Pathway analysis were performed based on the promoter enriched peaks (or promoter enriched differentially enriched regions) associated genes by ClusterProfiler R packages (v3.18.1).
Assembly: mm10
Supplementary files format and content: CUT&RUN.xlsx
Library strategy: CUT&RUN

growth_protocol: DMEM with 10% FBS

extract_protocol:
CUTANA™ ChIC/CUT&RUN Kit (EpiCypher) was used to streamlined chromatin profiling according to the protocol.
CUTANA™ CUT&RUN Library Prep Kit (EpiCypher) was used to streamlined chromatin profiling according to the protocol.

treatment_protocol: HEK293T cells were transient transfected with VGLL2-NCOA2, TEAD1-NCOA2 or YAP5SA palsmids.

value: Human embryonic kidney cells

value: TEAD1-NCOA2 overexpression

value: transient transfection TEAD1-NCOA2


title: Tumor-infiltrating immune cells, LNP-circRNAEV 1

description:
treatment(LNP-circRNAEV)
GZ23100894


title: Tumor-infiltrating immune cells, PBS control 2

description:
control
GZ23100891

value: PBS treatment


title: TN_P300_1


title: VN_P300_2

value: VGLL2-NCOA2 overexpression

value: transient transfection VGLL2-NCOA2


title: Tumor-infiltrating immune cells, PBS control 1

description:
control
GZ23100890


title: control diet, liver endothelial cells, biol rep 1

city: La Jolla

first: Caterina

last: Profaci

address: 9500 Gilman Drive

institute: University of California, San Diego

data_processing:
Raw paired-end sequencing data were aligned to the mouse genome (mm39 – UCSC Genome Browser) using STAR (v2.7.10a).
Gene counts were obtained using the featureCounts function from the R package Subread (v2.0.1).
Differential expression analysis was performed using default settings with DESeq2 (v1.32.0) in R (v4.1.0).
Assembly: mm39
Supplementary files format and content: excel file contains TPM values as well as DESeq2 statistics results

source_name: liver

extract_protocol:
Mice were anesthetized with ketamine/xylazine and decapitated. One lobe of the liver was dissected.  A series of enzymatic and mechanical steps was used to achieve a single cell suspension of the liver tissue. FACS was used to enrich for CD31+ endothelial cells, which were sorted into trizol for RNA extraction. RNA was extracted using the RNeasy Micro kit from Qiagen
Non-stranded mRNA libraries were made using Illumina's TruSeq RNA Library Prep Kit v2 according to manufacturer's instructions.

treatment_protocol: Mice were kept on control or PLX5622 (1200 ppm) diet for one month

value: liver

value: sorted endothelial cells

value: control diet

tag: treatment duration

value: 1 month


title: control diet, liver endothelial cells, biol rep 3


title: PLX5622 diet, liver endothelial cells, biol rep 1

value: PLX5622 diet, 1200 ppm


title: YAP_FLAG_1

value: YAP5SA overexpression

value: transient transfection YAP5SA


title: YAP_FLAG_2


title: PLX5622 diet, liver endothelial cells, biol rep 3


title: PLX5622 diet, male, biol rep 3

source_name: brain

extract_protocol:
Mice were anesthetized with ketamine/xylazine and decapitated. Brains were removed, meninges were peeled off, and cerebellum and olfactory bulbs were discarded.  A series of enzymatic and mechanical steps was used to achieve a single cell suspension of the remaining brain tissue. FACS was used to enrich for CD31+ endothelial cells, which were sorted into trizol for RNA extraction. Total RNA was extracted using the RNeasy Micro kit from QIAGEN.
Non-stranded mRNA libraries were made using Illumina's TruSeq RNA Library Prep Kit v2 according to manufacturer's instructions

treatment_protocol: Mice were kept on control or PLX5622 (1200 ppm) diet for one month.

value: brain


title: WT_P300_2

value: Wild Type

value: transient transfection pcDNA3.1


title: PLX5622 diet, liver endothelial cells, biol rep 2


title: WT_P300_1


title: VN_P300_1


title: VN_FLAG_2


title: PLX5622 diet, female, biol rep 2


title: WT_IgG_2


title: control diet, liver endothelial cells, biol rep 2


title: GFP2

data_processing:
ATAC-seq bioinformatics data analysis was performed following Harvard FAS Informatics ATAC_x0002_seq Guidelines. Briefly, fastp software (v0.20.0) was used to trim adaptor and remove low quality reads to get high quality clean reads. Then these clean reads were aligned to human reference genome (hg38) using bowtie2 software (v2.2.4). ATACseqQC R package (v1.22.0) was used to calculate and plot the fragment size distribution. Deeptools software (v3.5.1) was used to calculate and plot the correlations. Genrich software (v1.30.3) was used for peak calling and blacklist regions were removed. ChIPseeker R package (v1.30.3) was used to annotate the enriched peaks. Homer software (v4.11) was used to identify motifs. MANorm2 R package was used to perform differentially enriched region analysis between two groups of samples. GO and KEGG Pathway enrichment analysis were performed with ClusterProfiler R package (v3.18.1) based on the enriched peak and differentially enriched region_x0002_associated genes. And the enriched peaks were visualized in IGV (v2.64) software.
Assembly: mm10
Supplementary files format and content: ATAC.xlsx

extract_protocol:
Nuclear extraction kit (Solarbio) was used to prepare the library.
Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme) was used to prepare ATAC-seq library according to the protocol.

treatment_protocol: HEK293T cells were transient transfected with VGLL2-NCOA2, YAP5SA or GFP plasmids.

value: GFP

value: transient transfection GFP


title: control diet, female, biol rep 2


title: VN2

value: Human embryonic kidney cells


title: YAP5SA2


title: PLX5622 diet, male, biol rep 1


title: PLX5622 diet, male, biol rep 2


title: PLX5622 diet, female, biol rep 1


title: VN_FLAG_1


title: WT_IgG_1


title: control diet, female, biol rep 1


title: control diet, male, biol rep 3


title: control diet, male, biol rep 2


title: VN1